Spain midfielder Isco tapped in a rebounded shot from Cristiano Ronaldo to open the scoring in the 12th minute in Real Madrid's first visit to Catalonia this season amid the worst political crisis in Spain's 39 years of democracy.
The home side struck the woodwork twice before the break but rallied in the second half and Uruguay international Christian Stuani fired them level in the 54th minute.
Forward Portu then turned in the winning goal four minutes later to the delight of the 13,500 fans crammed into the Montilivi stadium.
Stuani came within inches of scoring again midway through the second half but a one-goal advantage was enough to give Girona their third win in their first campaign in the top flight and inflict a second league defeat on Zinedine Zidane's side.
Real are third in the standings on 20 points, four behind second-placed Valencia while unbeaten leaders Barca have 28.
Real coach Zidane blamed his side's lack of concentration for both of the goals they conceded.
"We did well in the first half but football is about details and the first goal was from a throw in and we weren't focused," he told a news conference.
"I don't think we played badly, we didn't lack intensity or effort, we just lost focused at the most important moments and that's why I'm annoyed.
"We're eight points behind but it won't change anything, we can pick ourselves up, we'll have better days than this and our rivals are going to drop points."
Although Real Madrid have many supporters in Catalonia, they are viewed as the club that is most representative of Spain and the arrival of the team bus at Montilivi was greeted with a smattering of boos and pro-Catalan independence flags.
POLITICAL HEAT
The political heat intensified two days before their visit when the region's ruling party declared independence from Spain and the central government responded by dissolving the Catalan parliament.
Deposed Catalan president Carles Puigdemont is from Girona province and a Girona supporter. He was not present at the game but showed his delight at the result with a post on Twitter.
"Girona's victory over one of the best teams in the world can be an example and a reference for many situations," he said.
Despite the political undertones, the atmosphere was no more intimidating for Madrid than any other Liga ground and they were cheered on by hundreds of supporters who mixed with the home fans without any trouble.
Pablo Maffeo, the Manchester City loanee who gained fame for his man-marking job on Lionel Messi, provided the first flash point of the game when his searching cross from the right wing pinged off the far post.
The ball remained in play and Madrid surged up the other end where Ronaldo fired at Girona goalkeeper Yassine Bounou and Isco was ideally placed to tap in the rebound.
Girona's fighting spirit could not be crushed, however, and they staged an incredible turnaround to record arguably the most significant win in their 87-year history.
"We fully deserved it," said Girona coach Pablo Machin.
"The fans have been behind us a long time, we promised we’d let them enjoy La Liga and today was the best atmosphere. If you’d said to me three years ago the fans would leave singing after beating Real Madrid I’d have said you were crazy."
(Reporting by Richard Martin; Editing by Christian Radnedge and Pritha Sarkar)
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