Unai Emery's men bounced back from successive 3-2 defeats by Barcelona and Celtic to claim three points which lifts them above their Portuguese rivals in the standings
The hosts open the scoring with less than three minutes played, with Rafael Carioca finishing off a wonderful breakaway from deep inside their own half, but their Portuguese opponents leveled matters courtesy of a near-post header from Lima half an hour later.
Benfica's Jardel, under pressure from Ari, put the ball in the back of his own net shortly before halftime, and Spartak held on to its slender advantage in the face of incessant late pressure from Benfica to register the club's first points of the Champions League campaign.
Spartak, who had blown 2-1 leads in its opening two games against Barcelona and Celtic, made a storming start and could easily have been ahead inside a minute, with Ari picking out Diniyar Bilyaletdinov unmarked in the area only for Artur to parry the former Everton man’s towering header away to safety.
Still, the home fans did not have to wait much longer to see their side go ahead. Bilyaletdinov pounced on a loose pass from Nemanja Matic in Spartak territory and surged forward before moving the ball onto Jurado. The on-loan Schalke attacker held it up superbly, waiting until the last possible second before slipping the supporting Rafael Carioca in on goal. The Brazilian demonstrated just as much poise and composure in drawing out Artur before coolly prodding the ball past his compatriot.
It should have been 2-0 not even 20 minutes later, but Ari volleyed against the bar after being picked out at the back post by a terrific cross from Jano Ananidze. Almost inevitably, the striker’s profligacy was punished almost immediately, as Lima headed home an equally inviting delivery, this time from Salvio from wide on the right after Spartak had failed to fully clear a Benfica corner.
The momentum appeared now very much with the visitors but, credit to Spartak, the hosts reclaimed the lead when Jardel bundled a dangerous cross from Evgeni Makeev into his own net, after the latter had been released into space by a defense-splitting pass from his captain, Dmitri Kombarov.
Despite dominating territory and possession in the final quarter, winless Benfica would not go so close again to snatching a point, meaning the Portuguese side drops to the bottom of the group and must now triumph in its return clash with Spartak in Lisbon to retain any realistic chance of reaching the last 16.