In a one-sided first half, fine goals from McGeady and Georgios Samaras gave the home side a deserved interval lead.
However, before substitute Niall McGinn scored the third after replacing Paddy McCourt, McGeady was booked by referee Willie Collum after clashing with James Fowler inside the Killie box, a decision which had Mowbray moving over to the Rugby Park management team of Jim Jefferies and Billy Brown to engage them in discussion.
"It is a frustration," Mowbray said.
"Every time someone goes down in the box it can't be a penalty or a booking.
"It's unfair on Aiden, he's maybe getting an unfair reputation and let's hope that is not the case.
"I work with him every day and you have to realise what type of player he is.
"He is fast, swift-footed and he dances with the ball between players.
"I thought the referee was very good today, he got around the pitch and did his job very well.
"So I'm not complaining that it was a penalty but like Easter Road, I didn't think it was a booking.
"I haven't watched it back but what I do know is that there was some body contact against a diminutive guy who has quick feet.
"What I'm saying is get on with the game."
Jefferies concurred with Mowbray on the McGeady incident, saying. "I agree with Tony, it wasn't an argument we were having.
"I don't think it was a booking and I didn't think it was a blatant dive.
"My first reaction was that it might be a penalty but I knew James Fowler is good at reading those things.
"And Tony is right, you don't always have to book the player so I think it was harsh."
With just two home wins in nine before the visit of Killie, which included a Co-operative Insurance Cup defeat by Hearts in midweek, Mowbray's side were under pressure to arrest their poor form at Celtic Park.
However, the Hoops' boss insists the only thing that separated the last two performances were the goals.
He said: "I genuinely judge my team on performance levels and if you watched the game on Wednesday, it was a similar performance.
"We controlled the game, created numerous chances but we hit the post, their keeper made some saves, the ball went past the post and we didn't win the game.
"This time we got the goals."
Jefferies had no complaints about the result although he revealed skipper Kevin Kyle admitted he should have scored a hat-trick with three headed chances in which he failed to hit the target.
"Celtic started the game unbelievably well and they would have beaten most teams on that performance," the Killie boss said.
"They could have been out of sight.
"We didn't get near them, when we got the ball we lost it too quickly but football is a funny game and Kevin Kyle thinks he should have had a hat-trick.
"At 2-0 he could have made it 2-1 and we could have had a lift.
"But at the end when we were leaving gaps they could have had a few more.
"So there are no complaints, Celtic deserved to win."