It was Lennon's 13th successive SPL win as Hoops manager - his fifth this season - but it came only after Conor Sammon had given Killie a shock lead after only seven minutes, the first goal the Hoops had conceded in the league.
"We were wasteful in possession early on, and ill-disciplined in our defensive shape at times," Lennon said.
"The goal was preventable, we got rolled in midfield and Glenn Loovens turned his back and Sammon got across him and tucked it in.
"Sooner or later we were going to concede a goal and it was the reaction that we were looking for and we got that.
"I'm delighted that we showed a lot character and as the game wore on, we got stronger and stronger.
"I thought we totally dominated the second half but it's always difficult to break a team down when they set up defensively like that."
Lennon had sympathy for McCourt who started for the first time since injuring his neck against Inverness on the opening day of the season, only to come off with a shoulder problem after 21 minutes.
The former Celtic skipper said: "He felt something go in his shoulder and we have to wait and see how he is tomorrow.
"It seems to be stop-start for him.
"Since he's come here it's been one step forward and two steps back.
"But in the last few weeks he has looked really fit and healthy.
"It's a blow for him and blow for us and we are hoping it won't be too serious.
"Hopefully he won’t be out for too long because we will miss him."
Lennon was pleased to see Stokes get off the mark in a Celtic jersey - then explained why he had dropped him.
"I like his style, he has the hunger to run in behind defenders, he is a fit boy and he will score goals for you," he said.
"Why did I leave him on the bench? That's a good question. We felt that with James Forrest being out and being away from home, we would put an extra midfielder in.
"Obviously when Stokes came on he added a bit of danger and he made a difference."