Hakimi was given a spot at right-back, and Jesus Vallejo was fit to start alongside Nacho at centre-back. Further forward, Marco Asensio and Lucas Vazquez came into the XI as Isco dropped to the bench.
Sergio Rico was also given the nod between the sticks over David Soria, while Lionel Carole was preferred to Johannes Geis at the back. Once again there was no spot in the squad for Steven N'Zonzi as the midfielder continues to be linked with a return to the Premier League.
Lucas Vazquez came close to sending Real Madrid ahead in just the second minute of action, but the winger's curling effort from the edge of the box was saved by Rico.
The home side did take the lead from the resulting corner, however, when a mix-up between Muriel and Simon Kjaer allowed Nacho the chance to sweep the ball into the back of the net from close range.
Ronaldo had the opportunity to double Real Madrid's lead in the 10th minute when he worked some space in a dangerous position, but the Portuguese could not find a route past Rico.
Los Blancos were having the opportunities, but Sevilla were enjoying plenty of the ball as they looked to hit back, and Carole had a low strike deflected just wide of the post in the 15th minute.
Karim Benzema headed over the Sevilla crossbar in the 20th minute as the end-to-end nature of the match continued, and it was the type of contest where the second goal would be massive.
Sevilla were full of adventure as they looked for an equaliser, and that cost them down the other end as Ronaldo sent Real Madrid 2-0 ahead in the 23rd minute with a fine finish from an Asensio pass.
It then went from bad to worse for Sevilla in the 31st minute when Jesus Navas conceded a penalty for handball inside the box, which allowed Ronaldo to step forward and send the home side three goals ahead.
Luka Modric and Ronaldo had chances to add to the scoring in the period that followed, and only some smart goalkeeping from Rico prevented Sevilla from conceding another two in quick succession.
Real Madrid did score their fourth in the 38th minute, however, when Kroos passed a low Lucas Vazquez cross into the back of the net following another counter-attack from the home side.
Four then became five in the 42nd minute when Hakimi raced onto a pass from Benzema before beating Rico at his near post to cap what was an incredible first half of football at the Bernabeu.
Sevilla had two decent chances to get their name on the scoresheet early in the second period, but Nolito curled one into the arms of Keylor Navas, before the Real Madrid goalkeeper got down well to keep out Muriel's effort.
The home side might have scored five in the first half, but Benzema was not on the scoresheet, and the striker's troubles continued in the second half as he had a weak attempt blocked just before the hour.
Benzema had another super chance in the 67th minute after meeting a cross from Marcelo, but the Frenchman's header smashed off the foot of the post.
There would be no hat-trick for Ronaldo as the number seven was brought off in the 76th minute, but it was a job well done for the home side as they overcame a couple of key suspensions and injuries to put another three points on the board.
Real Madrid (4-3-3): Navas; Achraf, Nacho, Vallejo, Marcelo; Kroos (Llorente 63'), Modric (Ceballos 71'), Asensio; Lucas, Benzema, Ronaldo (Isco 76')
Sevilla (4-3-3): Rico; Mercado, Carole, Kjaer, Lenglet; Pizarro, Banega (Krohn-Dehli 81'), Vazquez (Geis 71'); Navas, Muriel, Nolito (Sarabia 57')