Carlo Ancelotti's side were then reduced to 10 men in the 79th minute when Vinicius Jr was shown a straight red card for slapping Valencia goalkeeper Stole Dimitrievski.
Barcelona top the LaLiga standings with 15 points, four ahead of Real Madrid and Villarreal. Girona are seventh on seven points.
Alexis Sanchez struck twice and created a goal for Neymar as Barcelona recovered from conceding early to maintain their perfect La Liga start with a 4-1 win at home to Real Valladolid on Saturday.
A bullet header from Nicolas Otamendi put Valencia on course for a 3-1 victory over Eibar in La Liga on Sunday that boosted their hopes of claiming a Champions League place.
Valencia's Paco Alcacer and Dani Parejo both hit doubles in a surprise 5-1 away thrashing of high-flying Celta Vigo in La Liga on Saturday.
Lionel Messi scored one penalty and missed another as his double helped Barcelona sweep Levante aside in the second half in a 4-1 victory on Sunday to maintain their perfect La Liga start.
Real Madrid and Barcelona pulled two points clear in La Liga when Cristiano Ronaldo set a club scoring record in Real's 3-0 stroll against Levante and Neymar hit four as Barca beat Rayo Vallecano 5-2 on Saturday.
Real Madrid returned to winning ways after last weekend's drubbing at Atletico but failed to convince and were whistled by their own fans during a drab 2-0 victory at home to Deportivo La Coruna on Saturday.
A toothless and haggard Real Madrid slumped to a humiliating 10th Liga defeat of the season on Sunday as they lost 1-0 at struggling neighbours Rayo Vallecano.