Ronaldo added two more either side of registering an assist for Lucas Vazquez to complete his hat-trick in the second half, but Girona refused to go down without a fight and Stuani doubled his own personal tally to make it 4-2.
Gareth Bale and Juanpe then traded late goals as both sides continued to pour forward before Ronaldo fittingly had the final say, adding his fourth of the night in stoppage time to cap off the memorable encounter.
Find out how all of the action unfolded courtesy of Sports Mole's minute-by-minute updates below.
In terms of pedigree and history there could not really be a greater chasm between these two sides, but they come into today's game separated by only three places in the top flight as Madrid have endured a poor campaign so far, whereas Girona have been La Liga's surprise package.
It promises to be a fascinating encounter in the Spanish capital as Girona look to do the double over the European champions, but before we take a closer look at both clubs let's first check out the team news...
Well, there are plenty of notable inclusions and exclusions in the Real Madrid starting XI this evening, with the headline news centering around Gareth Bale, who only makes the bench for Los Blancos.
Bale had been a doubt heading into the game, but his inclusion among the substitutes suggests that he is fit enough to feature should he be needed tonight. Instead, Zidane has opted to start Marco Asensio in his place.
The lineup suggests that Zidane may go for something similar to a 4-4-2 formation with Benzema and Ronaldo both leading the line, although Asensio is more than capable of turning that into the 4-3-3 we are more used to seeing from Los Blancos, while the likes of Bale and Isco on the bench would also suit that system better.
Ronaldo comes into this match having scored 13 goals in his last seven games across all competitions and a whopping 17 in his last 10 outings - a run of form which includes six braces, one hat-trick and three assists on top of that. He is unstoppable at the moment.
Nacho comes into the heart of the defence alongside Varane to replace Ramos, with Dani Carvajal and Marcelo making up an otherwise unchanged back four in front of Keylor Navas in the Madrid goal.
Modric and Kroos have both had fitness concerns recently, but the latter is the only one to start today as Modric has to make do with a place on that very strong bench of Madrid's. Casemiro's exclusion is also interesting, with Kovacic and Vazquez replacing those two in the starting lineup.
From tonight's starting XI only Pablo Maffeo - from Manchester City - and Johan Mojica - from Rayo Vallecano - are on loan, but on the bench they also have Stoke loanee Marco Muniesa, Michael Olunga from Guizhou Zhicheng and Aleix Garcia from Man City as well.
Stuani has scored 15 times in La Liga this season - a tally only five players in the entire league, and only Cristiano Ronaldo from Real Madrid, can beat. That includes the equaliser in the reverse fixture between these two sides too.
That means we are likely to see a three-man defence from the visitors - risky if Madrid opt for three up front - although in reality that will probably more closely resemble a five-man backline with Madrid expected to dominate possession.
Girona have been La Liga's surprise package so far, and the biggest surprise along the way came in the reverse fixture of this tie. It was a famous victory for Girona, but an embarrassing defeat for Real Madrid - one of five league losses they have suffered this season.
The very best Real can hope for in terms of domestic success this season is now second place, although as things stand they will begin this match 10 points off even that, with Atletico Madrid currently leading Villarreal.
Indeed, before they can begin to think of that they must first focus on regaining third place this evening, which only a win will be enough to achieve. Madrid dropped down to fourth yesterday by virtue of Valencia's win over Alaves.
PSG were considered among the favourites themselves before that tie, which Madrid won 5-2 on aggregate, and they will face another difficult test in the quarters having been drawn against Juventus - another one of Zidane's former clubs.
Madrid have scored a whopping 35 goals over that 10-game spell in La Liga - an average of 3.5 per game - and have won six of their last seven outings in the league.
Indeed, Madrid have kept only one clean sheet from their last 13 outings across all competitions, and it is the same record in La Liga alone in a streak which stretches back to December 9. It is an area of their game where they simply must improve.
In La Liga alone that scoring record improves to 19 goals in their last four games - an average of 4.75 per game - but they have lost as many home outings in their last 12 La Liga outings as they had in their previous 57, so there is no longer an air of invincibility around the Bernabeu.
Many may have expected them to go straight back down or at least be fighting for their lives against relegation zone - particularly after only coming up as runners-up in the Segunda Division last season - but as it is they sit a full 22 points clear of the bottom three.
Girona come into this match sitting seventh in the table and Sevilla's defeat at Leganes earlier today means that victory at the Bernabeu would see them climb up to sixth - a position which would see them into the Europa League next season. Should they achieve that then it would be a truly remarkable feat.
Even so, the fact that we are even talking about Girona in the same breath as the likes of Sevilla and Villarreal is testament to how impressive they have been this season.
However, they have done brilliantly to stay in the top half and come into this match in superb form having won four of their last four games, including each of their last three - identical form to Real Madrid's over the last five games.
Another clean sheet tonight would see them keep four in a row for the first time ever in La Liga, and should they pull off a famous victory then it would be four La Liga wins in a row for the first time ever too. Girona's only previous run of three top-flight wins on the bounce also included that memorable win over Madrid in the reverse fixture, incidentally.
That victory did come in their most recent away game, though, as they recorded a very impressive 2-0 win at Villarreal, meaning that another win here would hand them back-to-back triumphs on their travels for only the second time this season.
Even so, their best form is at home, where they have remarkably won all of their last six La Liga matches without conceding a single goal in the process. Away from home Girona have drawn with Atletico this season, but they were soundly beaten at Barcelona whereas at home they have beaten Real Madrid and also drawn against Atletico.
Girona have been so impressive this season that it is hard to back against them, but when it is Real Madrid at the Bernabeu then that is a different story. Their title hopes may be long gone, but they are in good form at the moment and Ronaldo is back firing on all cylinders. I'm going for a comfortable home win.
SPORTS MOLE SAYS: Real Madrid 2-0 Girona
Today's visitors pulled off the biggest result in their history when the two sides first met in October, falling behind to an early Isco strike only for Stuani and Portu to respond in the space of four second-half minutes and seal a famous win for Girona.
The odds are against them, of course, but they will still fancy their chances and should come into this match full of confidence following their recent form.
However, Girona have also scored seven goals in that period of games this season, which is a tally only two teams - one of whom is Real Madrid - can beat, so we should be able to expect a quick start tonight.
REAL MADRID STARTING XI: Navas; Carvajal, Varane, Nacho, Marcelo; Kroos, Kovacic, Vazquez; Ronaldo, Benzema, Asensio
GIRONA STARTING XI: Bounou; Ramalho, Espinosa, Juanpe; Maffeo, Pons, Graneli, Mojica; Portu, Stuani, Garcia
Kroos plays a corner short before getting the ball back and picking out Ronaldo with a loss pass into the area. Ronaldo's movement earns him a yard, and that is all he needs to steer his finish into the bottom far corner.
The ball is swung into the area and Stuani meets it with a thumping header having lost his marker inside the area. Navas stood no chance!
The hosts have seen the vast majority of the ball as expected, but Girona have held their own and have had chances of their own as well which could have even seen them go into the break ahead. It is all to play for in the coming 45 minutes!
Ronaldo made it look simple on his weaker left foot - if he has a weaker side - but it was anything but as the ball was arriving to him at some pace from Kroos's pass.
It was a thumping header from Stuani for his 16th league goal of the season as he lost Carvajal before planting his finish into the corner, leaving Navas no chance in the Madrid goal.
There have been chances for the hosts aside from that, but Girona have also looked dangerous when coming forward and this one is still balanced on a knife edge. Can Girona pull off the league double over Madrid in their first ever top-flight campaign?
It is a really good move from the hosts as Kovacic gives the ball to Benzema, who in turn pokes a clever pass into the path of Ronaldo. Ronaldo's pace takes him away from the defence, and from that point there is only one outcome as he slams his effort in off the underside of the crossbar.
Real Madrid add a third to perhaps put this game to bed as Vazquez finishes off a really good team move. Marcelo finds Benzema down the left flank and the Frenchman plays a low ball in to Ronaldo, who collects the ball with his back to goal. He has a bit of space to work with, but unselfishly tees up Vazquez, who passes his finish into the bottom corner.
The ball is played in to Benzema, who really should score himself having collected possession in space inside the box. He has time to pick his spot but sees his effort saved by Bounou. However, the ball only bounces to the feet of Ronaldo, who slams the rebound in from close range.
Stuani gets his second of the night as he again beats Carvajal to the ball inside the box, diverting his header past Navas and in. This time the contact is much less clean, but Navas is wrong-footed and the ball bobbles in for give Girona their second.
Modric slides a pass through for Bale, who beats an untidy offside trap before sweeping his finish past the keeper, who got a touch but could not keep it out.
All three have been headers too, with Juanpe this time rising unmarked inside the area to plant a header home from a corner.
Ultimately Ronaldo was the difference tonight with a four-goal haul to continue his incredible recent goalscoring form, while Vazquez and Bale were also on the scoresheet for the hosts. Girona never gave up, though, and a brace from Stuani and Juanpe saw them fight right to the end in this thrilling contest. They very much played their part here tonight!
Thank you very much for joining Sports Mole for this incredible match as Real Madrid beat Girona 6-3 courtesy of four goals from Cristiano Ronaldo. I will leave you with our match report, and be sure to stick around for any reaction on site too. From me, though, it is goodbye for now!