The away side fell 2-0 behind after goals from Balazs Dzsudzsak and Jeremain Lens in the opening 25 minutes in Holland, but a volley from defender Anderson Luisao and a second-half Oscar Cardozo penalty secured Benfica's passage into an all-Portuguese semi-final against Braga.
Benfica were the quickest out of the traps and an improvised volley from Nicolas Gaitan almost gave the visitors an early breakthrough.
Javier Saviola was then gifted a great chance to break the deadlock after 10 minutes when PSV defender Antonio Marcelo played a ball across the defence straight into the path of the Argentinian but PSV goalkeeper Andreas Isaksson made a good save.
Despite requiring three goals to progress, the home side had been dominated in the opening exchanges but they started to impose themselves on the game and took their first real chance on 17 minutes.
Lens beat the Benfica offside trap and his pace allowed him to escape any challenges before he delivered a low cross which was converted by Dzsudzsak at the back post.
Lens again used his blistering pace to beat the visitors' defence on 25 minutes and when his first effort was well saved by Jimenez Roberto, the forward showed great composure to convert the rebound.
Dzsudzsak then had a great chance to put PSV in charge of the tie as he gathered possession on the edge of the box after a mistake from Maxi Pereira, but Roberto made himself big and blocked the shot.
The home side were starting to dominate and their defence were repelling anything that Benfica could throw at them, with only a long-range chip from Cardozo coming close.
But deep into first-half stoppage time Pereira swung in a free-kick which Isaksson flapped, at allowing Luisao to score an acrobatic volley and give Benfica a vital away goal.
The second half started slowly, with the first real chances of note coming just before the hour mark when Gaitan stung the palms of Isaksson and Luisao headed the resulting corner just over the bar.
Benfica's equaliser on the night came in the 62nd minute after Cesar Peixoto was crudely fouled in the box by Marcelo, who was lucky to remain on the pitch having already been booked, and Cardozo coolly slotted the penalty straight down the middle of the goal to put the tie beyond PSV.
PSV 2-2 Benfica: Match Report - view commentary, squad, and statictics of the game as it happened.