Roger Marti had cancelled out Benzema's first-half spot kick to leave the two teams on terms, but Bale netted 12 minutes from time to secure all three points for the European champions.
Madrid remain third in the table, but are now just two points off second-placed Atletico Madrid and nine points behind leaders Barcelona with 13 league games left.
Marcos Llorente was the only first-team player missing from Madrid's final training session ahead of this match. Indeed, Isco was able to train with the main group following a back problem, but the Spaniard was not in the squad.
As for Levante, Marti and Jose Luis Morales had 17 league goals between them this season ahead of the match and started as the front two, while Erick Cabaco could return to the back four following a suspension.
No team in Spain's top flight has conceded more goals than Levante this season. Indeed, a total of 45 conceded represents the worst record in the division and after a slow start, Madrid just started to force the issue in the 10th minute.
Morales wanted a penalty just before the 20-minute mark when he went down under a challenge from Carvajal, but neither the referee nor VAR were interested and on second look, it appeared to be the right decision.
Three minutes later, Marti hit the post for the home side, with the number nine coming in at the far post to meet a flicked header from Cabaco during a period of serious pressure.
Madrid were finding it difficult to deal with Morales's pace and movement as the 30-minute mark came and went.
Another excellent chance for the home side arrived in the 31st minute when Rober Pier broke onto a loose ball inside the box, but the defender somehow fired over from close range, before Levante goalkeeper Aitor Fernandez kept out a low strike from Vinicius down the other end.
Courtois then had to keep out a flicked effort from his own teammate Raphael Varane in the 36th minute as the pressure from Levante continued, with Morales and Marti both starring for the home side.
Madrid had two opportunities to take the lead in the latter stages of the first period, but Aitor kept out a low strike from Toni Kroos before collecting a loose effort from Vinicius moments later.
Los Blancos did score in the 43rd minute, however, with Benzema converting from the penalty spot.
Initially the handball from Enis Bardhi had been missed, but VAR intervened before the referee ultimately awarded the spot kick, which saw Madrid take a one-goal lead into the half-time break.
That was almost not the case, though, with Levante having a stunning chance to level in the 45th minute; Marti had the opportunity inside the Madrid box, but his low effort hit the post.
Marti had another opportunity moments into the second period, but the Levante attacker saw his effort from inside the Madrid box saved by the legs of Courtois.
Benzema was next to come close in the 55th minute, with the Frenchman seeing his header from a Kroos free kick just loop over the home side's crossbar during an end-to-end period of the match.
Levante were finally level on the hour, though, with Marti turning a low Morales cross into the far corner of the net. It was no more than the home side deserved for their application in the first 60 minutes.
Vinicius had a golden chance to send the visitors back ahead in the 71st minute, but the Brazilian - having raced clear of the Levante defender - could not find a route past Aitor.
Bale was introduced for the final 15 minutes of action and sent Madrid ahead just moments after entering the field.
Indeed, the visitors were awarded a penalty when Cheick Doukoure kicked Casemiro inside the box, which led to Bale rolling his spot kick into the back of the net before shrugging off the congratulations of his teammates.
Madrid finished the game with 10 men as Nacho picked up his second yellow card in the 86th minute for a foul on Raphael Dwamena, but the visitors held on to collect all three points against a Levante team who ended with 11 men but saw Rochina, who was sitting on the bench, sent off late on following a discussion with the referee.
Next up for Madrid is the second leg of their Copa del Rey semi-final at home to Barcelona on Wednesday night, while Levante will attempt to return to winning ways in the league when they travel to Leganes on March 4.
LEVANTE (3-5-2): Aitor; Rober, Vezo, Cabaco; Luna, Bardhi (Vukcevic 89'), Campana, Rochina (Doukoure 60'), Simon; Morales, Marti (Raphael 73')
REAL MADRID (4-3-3): Courtois; Carvajal, Nacho, Varane, Reguilon; Kroos (Valverde 69'), Casemiro, Modric; Lucas, Benzema (Bale 74'), Vinicius (Asensio 83')