The Magpies headed into tonight's second leg needing to score twice without reply to progress, and that looked achievable when Papiss Cisse put them ahead with 20 minutes left to play.
However, Eduardo Salvio broke Newcastle hearts in stoppage time when he capped off a counter-attack with a confident finish to ensure that the game finished 1-1.
Here, Sports Mole takes a closer look at the action to establish whether it was a fair result.
On target 6
On target 6
Was the result fair?
There is no doubt that Benfica were the better team over the two legs. They outplayed Newcastle on home soil, and controlled lengthy spells of the return leg. Although the Magpies showed some spirit at St James' Park, the Portuguese outfit would have been very hard done by had they stolen a second goal.
Alan Pardew's side were outclassed in the first leg, and on the back foot for the first 45 minutes of the second. They came alive in tonight's second leg and really pushed Benfica, but the gulf in quality between the two sides was always evident.
Benfica played with flair and tactical prowess throughout the two legs. They dominated the first 45 at St James' Park tonight and were unlucky not to go into half time with a lead. They had a few nervy moments in the second period, but deserve their stoppage-time equaliser when the share of possession is taken into account.
Sports Mole's man of the match
Nicolas Gaitan: Benfica's Argentine midfielder was more than Newcastle could handle this evening. He caused them all sorts of problems whenever he ventured forward and played a vital part in the goal that killed the tie off.
On a relatively gaffe-free evening, this award should go to Newcastle's sloppy defending in stoppage time to allow Benfica to nick that late goal. Even though scoring that vital second looked beyond the hosts, the last thing in the world they wanted to do was concede.
Croatian referee Ivan Bebek had a busy evening, handing out three yellow cards to each side. While some were perhaps more than called for, others were soft, but none of the questionable calls would have had an impact on the overall result.
Newcastle: Newcastle have a vital derby clash with Sunderland to contend with in their next Premier League fixture, where passions will no doubt be running even higher than they were tonight.
Benfica: Benfica are also in derby action, taking on bitter rivals Sporting Lisbon in their next domestic fixture.