Azzedine Ounahi fired the hosts into a surprise lead before half-time, with Kylian Mbappe earning Madrid a point from the penalty spot.
After Barcelona beat Alaves on Saturday to move top of the table, Madrid needed a victory at Girona to reclaim top spot but now sit second, a point behind the champions.
Coach Xabi Alonso brought centre-backs Eder Militao and Antonio Rudiger back after injury and maintained Brazilian forward Vinicius Junior in attack alongside Kylian Mbappe, who scored four at Olympiacos in the Champions League in midweek.
Mbappe and Arda Guler fired off target for Madrid early on in a hotly-contested but scrappy clash, in front of a raucous home crowd.
A poor Trent Alexander-Arnold pass allowed Girona forward Vladyslav Vanat in but his pass was intercepted when he might have opted to shoot.
Girona goalkeeper Paulo Gazzaniga made a fine save to keep out Eder Militao’s header before Mbappe thought he had fired Madrid ahead.
However, the French superstar’s goal, flicked home from close range, was disallowed as the ball bounced off his hand before he scored.
Just moments later, Morocco international Ounahi fired Girona ahead, rifling home from just inside the area to stun their illustrious visitors.
Catalan minnows Girona have twice beaten Real Madrid at Montilivi since making their top flight debut in 2017 and for a while it looked like they were going to manage it again.
Real Madrid goalkeeper Thibaut Courtois made a stunning save to tip away Vanat’s drive across goal before Madrid fought back.
Vinicius had a goal disallowed for offside before he was clumsily felled in the box by Hugo Rincon.
Mbappe smashed the resulting penalty into the bottom left corner past Gazzaniga’s dive for his 14th La Liga goal of the campaign.
Vinicius curled narrowly over and Mbappe whipped a shot inches wide in stoppage time as Madrid could not find a winner. (AFP)
