However, Celtic's relentless pressure paid off as Derk Boeriggter scrambled home his first goal for the club in the first minute of stoppage time before Commons grabbed his second of the game with a tap-in two minutes later.
It maintains Celtic's five point lead at the top of the table and continues their 13 match unbeaten start to the defence of their title. And Lennon was delighted with the never-say-die attitude displayed by his side.
"The character of the team is fantastic," the Celtic manager said. "I think we can play better at home but it's difficult. It takes two teams to make a game and a lot of teams come here and try to be hard to beat and break down and the onus is on us to find a way to do that and we're doing it.
"The quality can be better but it will be better as the season goes on. We are unbeaten in 13 games which is a brilliant start to the season so I've no criticism of the team at all."
It is the second successive home game that the Hoops have left it late after Charlie Mulgrew scored a stoppage time goal to deny Dundee United victory in a 1-1 draw earlier in November. "You need patience at times. It's not always going to be free-flowing football," Lennon admitted.
"I know from my own days as a player here under Martin O'Neill and Gordon Strachan that you get games like that. There was many a time we won in the last minute of games at home and this team have got the same ingredients and I'm delighted with that."
Morale for Milan
The victory gives Celtic a morale boost ahead of Tuesday's crucial UEFA Champions League clash with AC Milan in Glasgow on Tuesday. The Hoops must defeat the Italian giants if they are to retain any hope of matching last year's feat of qualifying for the last 16 of the competition.
But Lennon was in positive mood ahead of the clash. "We will be very, very strong coming into the Milan game," the Celtic manager said. "James Forrest will be fit, Anthony Stokes will rejoin us on Monday and Mikel Lustig had a rest today so he will be fresh.
"Psychologically the win will give the players a massive lift. I don't think they need any motivating for Tuesday night, I think that comes from within. It is there for us and with a couple players coming back into the squad as well will make us stronger.
"They qualified last year so they know what it is about. They won their last game at home against Ajax and they played very well in the San Siro. I think Milan will be different as well and will have a couple of players back so I think all the ingredients are there for another great game."
Aberdeen boss Derek McInnes said it was a stronger desire to win rather than Celtic's quality that cost his side victory. "We are just looking for that determination to get ourselves in front and it was that sort of determination that got Celtic over the line and secured them the three points," McInnes said.
"It wasn't quality that beat us and I mean that with all due respect to Celtic. They have loads of quality players and they're playing here because they are winners and determined more than anything. And it was that determination to get the ball over the line that ended up beating us."