The Brazilian striker capitalised on some slack defending to give the Yellow Submarine a share of the spoils against Marcelo Bielsa's side in a back-and-forth encounter
The hosts had taken an early lead through Marcos Senna's free-kick, but were pegged back through second half goals from substitute Fernando Llorente and Markel Susaeta.
Nilmar then scored an equaliser to avert a second defeat in a row for the home side, who came into this match on the back of a 4-0 capitulation at Mallorca last weekend.
The hosts dominated possession in the opening stages, and their early pressure was rewarded when Bruno Soriano was brought down by Ander Herrera just outside the Athletic box.
Captain Senna curled the resultant free-kick sumptuously into the right-hand corner, giving goalkeeper Gorka Iraizoz no chance.
Lifted by the early goal, the Yellow Submarine looked to turn the screw on their opponents, who looked visibly lethargic after their midweek exploits in Europe, and could have extended their advantage soon after as Borja Valero fired a long range effort narrowly wide.
Senna could have doubled his tally when Martinez fouled Martinuccio in a position similar to the one which produced the first goal, but the Brazilian's curler was saved by the keeper this time.
Athletic gradually came into the game towards the latter stages of the first half, with Susaeta being the chief source of threat to the Villarreal goal down the right flank.
The Basque winger almost brought his side level when he won and almost converted a free kick, but Villarreal keeper David Lopez was up to the task.
Villarreal's momentum was briefly disrupted by a thigh injury to Ruben in the 38th minute, who was then replaced by Brazilian striker Nilmar.
Llorente was brought on at the start of the second half in place of the anonymous Lopez, as Bielsa looked to exploit the hosts' perceived vulnerability in the air.
The move almost paid immediate dividends when the striker escaped the attentions of the Villarreal defence, but could not direct Andoni Iraola's cross on target.
The Pamplona-born forward soon made amends for that miss, though, as he calmly headed Toquero's cross beyond the reach of David Lopez to notch his 12th league goal of the season.
The hosts were then made to pay for their profligacy in front of goal, with Susaeta scoring against the run of play after being sent one-on-one with the goalkeeper, after the hosts had conceded possession deep inside their opponents' half.
Los Leones barely deserved their lead on the balance of play, and they duly lost it after Martinez failed to intercept a forward pass and was made to pay as Nilmar capitalised to level the scores again.
Molina's side looked for a winner that would have lifted them five points off the drop zone, but it was the visitors who came closest through Llorente, whose close range shot was saved by David Lopez after a mix-up in the Villarreal back line.
The draw leaves the hosts just three points off the relegation spots, while Bielsa's side climb two spots to fifth, level on points with Malaga.