However, the Hibs boss confirmed that the Republic of Ireland striker is back in the squad for the Scottish Premiership game with Partick Thistle at Firhill on Saturday.
"It's been dealt with, so he is back in the squad," Lennon told reporters at his pre-match press conference.
"He didn't have to apologise. He just needs to understand there are certain codes of conduct and a level of discipline that you can't cross with me.
"It was an isolated incident. I was not going to tolerate it and he understands that. He is back in and has been training very well this week."
Stokes, 29, has scored nine goals in 14 appearances this season since rejoining Hibs last summer after one season with Blackburn Rovers.