Aberdeen beat the champions 2-1 at Pittodrie after Virgil van Dijk was given a straight red card in the 12th minute. Lennon was angry about that decision and also Thomson's refusal to give a penalty for a second-half handball by Mark Reynolds.
In fact the van Dijk decision was right - he brought down Peter Pawlett as the midfielder was bursting through on goal - although a penalty should have been given when the ball hit Reynolds's arm from a long throw.
An outstanding long-range goal from Jonny Hayes meant Fraser Forster's run without conceding an SPFL goal ended on 1255 minutes, and an Adam Rooney header had Aberdeen 2-0 up against the ten men at half-time. James Forrest pulled one back and a strong second half kept Celtic right in contention to the end, but eventually they went down and Lennon singled out the referee.
"I thought we were worthy of the win, I thought we deserved it," said Lennon. "The referee ruined the game. It's not a sending off. Pawlett's going across the goal rather than towards the goal and I'm pretty sure Efe Ambrose was getting across. There was a clear handball in the second half. The referee has seen it and said it wasn't deliberate.
"Everyone else in the ground must have known it was a penalty. He's had two crucial decisions go against us. I spoke to the referee briefly after the game, on the pitch. He didn't give an explanation - he just said he understood I was upset and left it at that. I think it's poor.
"I thought we were outstanding. The first goal you can hold your hand up and say it was a great hit. You don't mind that - it's going to take a special goal to beat Fraser. The second goal is disappointing from our point of view but I thought we were magnificent in the second half and I expect that from these players.
"They are an outstanding group of players with some outstanding individuals. We are disappointed the run has come to an end but they can be very proud of what they've achieved."
Lennon reacted sharply when he was asked if he welcomed the renewed challenge by Aberdeen this season (they also beat Celtic in the William Hill Scottish Cup earlier this month). "What, 21 points is a challenge?" he said, referring to Celtic's lead in the Premiership. "Aberdeen were good. They have been good for the full season: that's credit to Derek [McInnes]. He's done a fantastic job but my team were outstanding tonight. We have to keep going. We will give players games but I want to win the title soon and then plan for next season."
McInnes was understandably thrilled with his second win over Celtic this month. The result delivered another vivid result for Aberdeen in what promises to be a memorable campaign. "I'm delighted with every single one of the players," he said. "It's a good night for the club. You saw Pittodrie at its best, the supporters really energised and got behind the team. We deservedly won with two magnificent goals.
"It was the right decision by the referee to send Van Dijk off, Peter Pawlett was bright as a button again, spooking him and forcing that. We always feel we can score goals. We said at half-time 2-0 might be enough but we didn't want to play as deep as we did in the second half. If we had been a bit cuter we could have added to that tally. Celtic were proud of their unbeaten record, they've made that really clear for a long time now."