The Catalan derby rounded off the weekend’s action in Spain, with Barca aiming to continue topping the standings.
Girona found the first big chance as a corner to the back post found Bernardo Espinosa, but his firm header went straight to Marc Andre Ter Stegen on five minutes.
Messi came very close to breaking the deadlock after collecting on the edge of the box to beat three defenders on his way to a shooting position, but Yassine Bouno’s fingertip turned it around the post.
Barca broke the lead on 19 minutes after Arturo Vidal used strength to shrug off a defender before teeing up Messi to finish in the bottom corner.
Luis Suarez nearly made it two in as many minutes with some brilliant footwork to escape the defender, but he tried to give Bounou is not fooled at his near post which didn’t paid off.
Chilean Arturo Vidal fired towards the feet of Suarez, who flicked the ball into the path of Ousmane Dembele but the end result was easy for the keeper.
Girona were close to grabbing an equaliser after Portu raced on to a through-ball from Alex Granell but after taking it past the goalkeeper saw his finish cleared off the line by Gerard Pique.
Barca were given a blow when Clement Lenglet received his marching orders for an off-the-ball challenge on 38 minutes.
Girona’s resistance paid off just before halftime with Christian Stuani perfectly placed to poke home the equaliser on the stroke of halftime.
For the second half, there was no changes at either end with both managers happy with the first 45 minutes of work done by their playing personnel.
Stuani stunned the Camp Nou with his second after lashing a brilliant finish into the top corner with the keeper out of position on 51 minutes.
Barca made a double change nine minutes later, as Ivan Rakitic and Phillipe Coutinho replaced Arthur and Vidal respectively.
A minute later, Messi curled a free kick towards the top corner, but his brilliant effort clattered against the crossbar.
Eventually the score-line was level-pegging after a darting run to the near post by Suarez found his effort saved from a tight angle to which the ball rose for Pique to nod to an empty net.
The substation of Coutinho brought a bit of energy to the Barca attack and on quite a few occasions put the visiting side on their nerves.
Late on, a curler from outside the box by the Brazilian whistled agonisingly wide of goal as the Catalans settled for a draw.