With the match at 1-1 in the second half, after David Goodwillie had cancelled out Gary Hooper's opener before the break, McDonald pointed to the spot after Dusan Pernis dived at the feet of Hooper to prevent him going through on goal.
However, after consulting his assistant, Steven Craven, McDonald gave a bounce ball in the box.
Hooper scored a dramatic winner two minutes from time to extend the Parkhead side's winning run in the SPL to nine games ahead of next week's clash with SPL leaders Rangers.
"He's given the penalty and for me he can't change his mind," Lennon said.
"I didn't get an explanation until the referee came over and spoke to me.
"His explanation was that his linesman had a better view of it and the keeper had played the ball.
"I find that unacceptable. He looked pretty adamant to me when he gave the penalty. He got a really good look at it.
"Looking at the replay Pernis has got a touch on the ball but he has taken Garry as well.
"There was a long, long delay between him awarding the penalty and him allowing the bounce ball.
"It was a very strange decision and we could have got a couple of other penalties as well."
With some sarcasm, the former Celtic skipper added: "But I suppose you have to put it down to another honest mistake by the referee."
He said: "It was one of the best performances I've seen since I've been in charge of the team in terms of attacking, quality football.
"I'm very proud of the team and despite a very controversial decision going against us, they never let their heads go down, we kept creating chances and we got what we deserved.
"Some of our stuff was breathtaking and I couldn't ask for any more (ahead of next week).
"I watched Rangers on Saturday and they were very impressive in the second half.
"Both teams have shown a tremendous level of consistency so far and something has to give next week and it will be interesting."