The Bhoys began the game at a high tempo and surged ahead through Teemu Pukki before Charlie Mulgrew seemingly made the game safe with a second shortly before the half-hour mark.
Saints steadied their ship and fought their way back into contention as Liam Caddis' 81th-minute effort ensured a nervy finish, but Celtic held on to move level on points with league leaders Inverness with a game in hand.
"I'm not going to let the last 10 minutes detract away from what was for the first 80, a top performance," said Lennon. "For me, it was a natural course of events after midweek.
"There was mental and physical fatigue in the last 10 minutes which was totally understandable. We had no time to prepare for this game at all. It was all about recovery from Wednesday.
"I thought the first half we were fantastic, the best we've played this season and it was after a big Champions League game in midweek, so I take my hat off to the players, it is a big, big win.
"There was a flow to us, we were creating good chances. Anthony Stokes got one off the line, he flashed a shot wide, he looked half-decent on the counter attack.
"But 2-0 is obviously a funny scoreline. If St Johnstone get one then it is all hands to the pump as it were but as I said, I won't let the last 10 minutes affect what was for me, a very good performance."
Saints manager Tommy Wright added: "We didn't work hard enough in the first half. I don't know if the players showed them too much respect.
"I thought we were much better in the second half and truth to be told, we could probably grabbed a draw at the end."