The Mexico forward, a new signing for the team known as the Yellow Submarine, who return to the top flight after a season in the second division, marked his competitive debut by burying a low cross in the 83rd minute.
With four minutes to go he then carved the opening for Jonathan Pereira to grab the decider with a deflected shot, somewhat unfairly denying the hosts a share of the spoils.
Almeria had dominated for most of the game with two goals from striker Rodri, who netted in the 39th on a counter-attack, and in the 74th with a close range volley.
Villarreal had levelled at 1-1 in the 65th when Almeria defender Sebastian Dubarbier diverted a cross into his own net.
"Almeria were superior for much of the game but perhaps paid for their earlier efforts as they tired in the last 20 minutes," Villarreal coach Mareclino told a news conference.
Espanyol came back from two goals down to grab a 2-2 draw at Celta Vigo to deny new coach Luis Enrique and former Spain midfielder an opening day win.
Alex Lopez and Charles had scored for Celta either side of halftime, but Victor Sanchez and Thievy dampened the celebrations.
Earlier, Alberto Bueno spoiled Elche's return to La Liga after a 24-year absence by scoring twice to help Rayo Vallecano to a 3-0 home win.
The game started in bizarre circumstances as Rayo fans staged a silent protest against the football league's unpopular scheduling policy to suit television with games on Mondays and Fridays and 11 p.m. kickoff slots.
The protest ended in the 24th minute when the stadium came back to life and in the 40th former Real Madrid forward Bueno arrived late to drill a low shot into the corner.
Alberto Perea's spectacular long-range shot a minute before the break doubled the advantage and Bueno matched his team mate's strike with another 25-metre shot in the 74th.