The Dons took the points from St Mirren Park with an Adam Rooney penalty 10 minutes from time, after Eric Djemba-Djemba slid in to trip Peter Pawlett on the 18-yard line.
"Again it's another big decision that's gone against us I feel," said Lennon.
"The viewers at home will have the opportunity to debate whether it is inside or outside the box, and it's a big call from the referee with the position that he's in.
"I've only see it the once there and as I said, it feels like a decision that's gone against us.
"It's very much hard to take. It's one you can debate whether it's inside the box or not. But for a man of Eric's experience to make that type of challenge in and around that area is disappointing.
"The players went out there and did everything we had asked against a high-flying Aberdeen side."
Aberdeen assistant boss Tony Docherty admitted the team had to grind out a result, but he was delighted with the application of the visitors.
"It's important that we have that winning mentality and I think we had it today," Docherty said.
"We didn't play at our best, up to the level of performance in our previous games but we dug a result out.
"It went for us today, and we've come away from a difficult venue against a very dogged team who were set up to be that way and come away with three points, so we've done our bit."