The defeat was the second in less than a week for Barca (58 points) and left them second in the standings, two points behind their bitter rivals.
A win would have taken the defending champions back above Madrid, but instead a crisis brewed on Monday night for coach Hansi Flick, whose side lost to Atletico Madrid 4-0 in the Copa del Rey last time out.
The second defeat came even though Barcelona took the lead early in the second half.
Yamal hit the post with his spot kick on the stroke of halftime but 14 minutes into the second period Pau Cubarsi met Jules Kounde's cross from the right and placed his header perfectly into the top corner.
The goal was Barcelona's 100th in all competitions this season and made them the second club in Europe's big five domestic leagues to hit the century after Bayern Munich.
However, Girona roared back into the game just three minutes later.
Barca's Joan Garcia was already the busier of the two goalkeepers but he could not stop Thomas Lemar side-footing home from close range.
Both sides pushed for a decisive second and it was the hosts who executed with three minutes remaining, substitute Fran Beltran scoring with a low shot from just inside the box.
"We lacked a bit of everything. We need to be self-critical. We need to improve things and get our act together," Cubarsi told DAZN.
"After my goal, they scored very quickly to equalise ... We need to improve on those goals they score right after we take the lead."
Girona's Joel Roca was sent off in the dying seconds but there were no more goals.
The victory ended a three-game winless streak for Girona and lifted them three places to 12th. Only seven points separate eighth to 18th in La Liga.
With Reuters.
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