Lennon criticised Thomson's decision to send off Virgil van Dijk in the 11th minute for denying a goalscoring chance, after he brought down Peter Pawlett as the Dons winger tried to burst into the box.
Celtic had started well but they lost 2-1 with a man down and Lennon felt his side should have had a penalty for a handball by Mark Reynolds just before James Forrest pulled a 61st-minute goal back for the champions, who had been unbeaten in their previous 26 league games this season.
Lennon said: "I thought we were worthy of the win. I thought the referee ruined the game. It's not a sending-off. Pawlett was going across the goal rather than towards the goal. I'm pretty sure Ambrose would have got across.
"And there was a clear handball in the second half. He saw it and said it wasn't deliberate."
Lennon is considering an appeal against Van Dijk's dismissal and added: "I think it's poor. Maybe I am the only one who sees it that way but I have looked at it again and I'm pretty convinced it's not a red card."
The Celtic boss admitted there was nothing his side could do to stop the 30-yard opener from Jonny Hayes, which ended Fraser Forster's 1,256-minute run without conceding a league goal, but felt his defence could have done more to stop Adam Rooney's header making it 2-0 just before the break.
But he was full of praise for his side's second-half comeback attempts.
"I thought we were the better team first half, we had the better chances anyway," he added. "I said to the players: 'You can't let the run go now. Go out there and take the game to Aberdeen as much as you can.' And they did that. I thought they were fantastic.
"It looked like we had the extra man. We dominated and didn't get the rewards all our good play and mental strength deserved. But sometimes you don't get what you deserve in football."
Aberdeen manager Derek McInnes had a different opinion on the red card and felt his side were well worth their second victory over Celtic this month, having knocked Lennon's side out of the William Hill Scottish Cup at Parkhead.
McInnes said: "The fans have seen their team win and deservedly win with two magnificent goals and loads of effort from every single one of the players.
"It's not easy beating Celtic whether it's against 11 men or 10 men.
"You can see why these players play for Celtic, they never know they're beat. I thought they took full responsibility in the second half and the introduction of Forrest caused us problems.
"We were too deep and it was a bit disappointing that we never kept the ball better. When Celtic score it adds to the anxiety in the ground and belief of Celtic.
"But over the 90 minutes I thought we were the better side and created the better opportunities. It was the right decision to send Van Dijk off."
McInnes added: "We should celebrate a good night for our club because it's a big ask beating Celtic. They are proud of their unbeaten record. They have made that really clear.
"If we didn't get the credit we possibly deserved at Parkhead, I'm sure we'll get it tonight."