The 31-year-old, who made his third start in nine league appearances since joining the side in the summer, found the net but could not prevent the White and Reds from extending their winless run to eight games.
Quique Setien’s men started the game brightly with Cristian Tello grabbing the curtain raiser 12 minutes into the tie.
Aleix Garcia levelled proceedings for the visitors in the 36th minute before Doumbia put his side in front for the first time in the game eight minutes later – his third goal of the season.
Loren Moron restored parity to the home team in the 54th minute and Sergio Canales scored the winning goal at the death.
Despite the loss, Girona are 10th in the log with 24 points from 20 games. They take on Barcelona in their next league game on January 27.