The comeback will boost the Spanish side's confidence ahead of the Champions' League semi-final showdown with Arsenal next week.
Depor midfielder Sergio broke the deadlock in the 71st minute steering a side-footed shot just inside the post from the edge of the area. The Mexican striker Franco equalised when he was left unmarked to head home Marcos Senna's corner, and Villarreal missed a host of chances towards the end.
With one eye on the Arsenal tie, Villarreal dropped first-choice keeper Sebastian Viera to make way for Mariano Barbosa, who was signed in the summer to replace the Liverpool bound Jose Reina.
Viera is out of the first leg after being booked against Internazionale and so Barbosa played last night and will be used against Barcelona on Friday.
Barbosa started the season as the No 1 but Viera, rejected by Arsène Wenger, who had the chance to sign him a season ago, has played throughout Villarreal's Champions' League run and kept Barbosa out of the team.
The hard-running striker Jose Mari was rested but with their European campaign still vital for Villarreal, the Argentinian playmaker Juan Ramon Riquelme started. It is good news for Arsenal that the brilliant but occasionally leaden-legged midfielder, usually rested for games in La Liga ahead of Champions' League matches is being forced into a heavy programme of three games a week.
Villarreal's rivals Deportivo had only lost four times on their travels this season, although the last of those was a thumping 4-0 thrashing at the hands of Real Madrid.
They went into the game ahead of Villarreal and looking more likely to land one of the two Uefa Cup places. They had the first chance of the game through Victor who shot wide after creating space on the left, but the home side gradually took control of the game.
Marcos Sena shot wide on eight minutes with their first real chance and Diego Forlan went close following sloppy goalkeeping by Jose Molina but both sides had their best chances just before the break.
Arizmendi almost put Deportivo into the lead but his curled shot bound for the top corner deflected off Pedro Munitis wide for a corner.
Minutes later Forlan crossed for Gonzalo whose shot from the edge of the six-yard box went narrowly wide.
Villarreal (4-4-2): Barbosa; Javi Venta, Peña, Gonzalo Rodriguez, Arraubarrena; Sorin, Marcos Senna, Tacchinardi, Riquelme; Franco, Forlan. Substitutes: Sebastián Viera, Carzola, Josemi, Jose Mari, Cesar Arzo, Font, Roger
Deportivo la Coruña (4-5-1): Molina; Manuel Pablo, Collocini, Hector, Capdevilla; Sergio, De Guzmán, Victor, Lago; Munitis, Arizmendi. Substitutes: Dani Mallo, Cesar, Romero, Jesús, Rubin Castro, Diego Tristan, Xisco.
Referee: M Perez Lasa.
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