The hosts twice took the lead but were pegged back by subsequent equalisers from Diego Simeone's men, who needed the former Chelsea striker to secure a draw
The substitute rose to meet Koke's 80th-minute corner and his powerful effort crept past Diego Marino at the near post, to save Atletico from a disappointing defeat at Estadi Ciutat de Valencia.
Despite controlling possession early on in Sunday's clash, Atletico fell behind just after the half-hour as David Barral netted his 11th of the season from close range.
That lead was wiped out almost immediately, though, as Guilherme Siqueira registered his first Atletico goal with a neat volley from six yards.
Chances were few and far between early in the second half until Kalu Uche was presented with a chance, the Nigerian gratefully accepting at the second attempt.
Atletico's attempts to get back into the game looked to be coming up short, until Torres rose to score his third league goal since rejoining his boyhood club and edge them four points clear of Valencia in the race for a top-three place and qualification for the Champions League group stage.
The visitors made a positive start to try to break down the five-man Levante defence with Mario Mandzukic going close twice in the opening 10 minutes, his second attempt superbly saved by the legs of Marino.
Simeone's side were dominating in the opening exchanges, but looked fragile to the counter-attack, with Uche's pace a particular concern.
The forward was not needed as Levante took the lead in the 32nd minute, though, punishing slack defending to break the deadlock as Miranda's poor clearance fell to the unmarked Ivan Lopez and he rolled the ball across the six-yard box for Barral to tap home.
Conceding spurred Atletico into life and within three minutes they were level through Siqueira, the full-back capping off an impressive half with a well-executed volley from Tiago's chipped pass.
In a carbon copy of the first half, Atletico resumed control after the restart but were frustrated by Levante's well-organised backline.
At the other end Atletico's own defending was less impressive and with 63 minutes on the clock they gifted their hosts a second goal, Uche escaping the attentions of Jose Gimenez to bundle home Lopez's cross.
Simeone looked to Torres to spark the visitors into life, and the 31-year-old answered the call perfectly with a crucial goal to extend their unbeaten run to a 13th game.
The striker evaded his markers at the front post to meet Koke's delivery and ensure Atletico remain in the driving seat for a top-three berth.