Aubameyang was named among the substitutes at the Emirates Stadium but was introduced after just 30 minutes following a serious injury suffered by Danny Welbeck .
The Gabon international subsequently missed a number of chances as the Gunners failed to break down their Portuguese opponents, though the draw was enough to secure their place in the knockout stages.
Former Gunners defender Keown singled out Aubameyang for criticism after the game and feels there is still much more to come from the 29-year-old.
"Aubameyang really let them down a little bit in front of goal," he told BT Sport .
"He’s a player I rate really very highly. I think tonight with the injury it caught him out because he wasn’t ready mentally and I think on another night he would have put these chances away.
"He is the closest thing to Thierry Henry since he left that club. He really is that good.
"Someone should really be in his camp pushing him on, dragging him, drawing a performance out of him.
"Because he’s a special talent, scores lots of goals and it’s just a hunger. It’s getting to that boiling point and I don’t think he was there tonight."
Despite drawing a blank, Aubameyang, who joined from Borussia Dortmund for a reported £55 million ($72m) in January , still has nine goals in 14 appearances so far this season – including four from the substitutes bench.
His efforts in front of goal have helped Arsenal make an impressive start under new boss Unai Emery.
After losing their opening two matches of the season, Arsenal have won 12 and drawn three of their 15 games in all competitions since, including a run of 11 straight victories between August and October.
Thursday’s draw ensured they stayed three points clear of Sporting in Group H, with 10 points from four matches ensuring they are certain of a place in the last 32.
Emery’s men can secure top spot in the group with victory at Ukrainian side Vorskla Poltava on November 29.
Next up for Arsenal in the Premier League is a game against Wolves at the Emirates Stadium on Sunday.