Marcelino Garcia Toral's charges were able to take control of the game and weighed in with more chances but were unable to add to their tally come the break.
Early in the second half, Valencia were given the opportunity to take the lead from the spot after Jose Luis Gaya was brought down in the box.
Daniel Parejo stepped up and duly drilled home from 12 yards out, the hosts able to hold on for all three points against the Catalan side.
The result cements Valencia's hold on third place in the La Liga table, keeping them six points clear of fourth-placed Real Madrid, while Girona stay 10th in the standings.
VALENCIA (4-4-2): Neto; Vidal (Vezo 67'), Garay, Paulista, Gaya; Pereira (Maksimovic 82'), Parejo, Kondogbia, Guedes; Rodrigo, Mina (Vietto 74')
GIRONA (3-5-2): Bounou; Ramalho, Espinosa, Ramirez; Maffeo (Aday 65'), Pere, Timor, Granell (Borja 45'), Mojica (Moreno 74'); Portu, Stuani