Arsenal had dominated the first half but only created one clear-cut goalscoring chance. Pierre-Emerick Aubameyang missed an easy opportunity to break the deadlock, the Gabon striker unable to convert Hector Bellerin's cross from six yards when unmarked in the box.
Arsenal's play was neat and tidy but they always seemed to fall short in the final third. And they were punished when Benfica were gifted a penalty after Emile Smith-Rowe was adjudged to have handled the ball. Luis Pizzi converted from the spot.
Aubameyang had a fantastic chance to win the game but he could only drag his shot wide when through on goal, a move that summed up his, and Arsenal's evening.
The Gunners' movement behind Aubameyang was impressive, with Smith-Rowe, Saka and Martin Odegaard all linking well. Odegaard's range of passing in particular was superb.
Arsenal continue to press the self-destruct button at times. They played a needless ball across the face of goal before the break, while in the second half their failure to clear the ball and concede a corner led to the penalty that saw them go a goal behind.
Manager rating out of 10
6 - Mikel Arteta will have been frustrated by this result. His team had the better of the game and looked the more likely to score, but again he was left ruing a costly unenforced error. Also, he might have introduced more pace earlier, with several players looking tired.
Player ratings (1-10; 10 = best. Players introduced after 70 minutes get no rating)
GK Bernd Leno 6 - The Arsenal stopper didn't have much to do in the way of saves to make, but he certainly saw plenty of the ball. He was guilty of holding on to it for too long and slowing Arsenal's play. He could do little to stop Pizzi's penalty.
DF Hector Bellerin 6 - The Spaniard was an attacking outlet on the right flank, regularly hitting the touchline or box to get crosses into the area. His final ball often let him down, though; the exception was a cross for Aubameyang's chance in the first half.
DF David Luiz 6 - Was solid for the most part and was often in the right place at the right time to defend his lines. There were times he will have been grateful to Dani Ceballos for covering for him, but this was an event-free outing for the Brazilian.
DF Gabriel Magalhaes 6 - The Brazilian defender was a stable presence alongside David Luiz. He made some important interceptions and restricted Benfica's attacking options.
DF Cedric Soares 6 - Made way for Kieran Tierney in the second half, but not before playing his part in pulling Arsenal level. His run and subsequent cross allowed Saka to volley home the Gunners' equaliser.
MF Dani Ceballos 7 - The Spaniard was a solid presence in the middle. He covered well at the back and his passing was superb, one through ball in particular opening up Benfica and releasing Bellerin on the right. He was, however, sometimes guilty of taking too many touches and running into trouble when a pass would have been far more effective.
MF Granit Xhaka 5 - Not his finest evening. He played a particularly needless and careless cross-field pass just before the break that put his defence under unnecessary pressure. Overall there were too many sideways passes; he simply seems to struggle without Thomas Partey alongside him.
MF Bukayo Saka 8 - Was a danger all evening. He had an effort saved before the break, at which point he had been too often guilty of drifting offside. He was most effective when cutting in from the right hand side, and after having several shots on goal he finally found the net when he converted Cedric's teasing cross.
MF Martin Odegaard 8 - The loanee looked very good on the ball. His link-up play with those around him was impressive and his passing was a constant source of ammunition for Arsenal. One pass in particular, to Saka, will have Arsenal fans dreaming of a permanent move for the Norwegian.
MF Emile Smith-Rowe 6 - Link up play was as solid as ever, though he looked tired throughout. He played in a wider position than usual and he wasn't as effective as when he's played through the middle. Ran his socks off before being replaced.
FW Pierre-Emerick Aubameyang 6 - The skipper missed an absolute sitter following a delicious cross from Bellerin, and it just seemed to be one of those nights for him. He missed another one-on-one in the second half and then fluffed his lines by taking too many touches when through once again. Sharp, but not potent enough.
DF Kieran Tierney (Soares, 64) 7 - Tierney linked up well with Nicolas Pepe on the left-hand side and he did the simple things well. Arsenal will be delighted to have him back.
FW Nicolas Pepe (Aubameyang, 77), N/A - Looked dangerous when he came on, though a heavy touch undid some good work from Tierney with the Gunners in a dangerous position.
MF Gabriel Martinelli (Smith-Rowe, 77) N/A - Back in action after a long lay-off, Martinelli didn't see much of the ball in the closing stages.
MF Willian (Odegaard, 90) N/A - The Brazilian had very little time to make an impact.
DF Mohamed Elneny (Ceballos, 90) N/A - Had a couple of touches but only had four minutes of injury time on the pitch.