The Belgium defender, subject of a failed £9 million bid by Fulham before the English transfer window closed, had posted a video of himself receiving treatment before the game in Greece.
His agent Jacques Lichtenstein was quoted earlier in the week by DH.be saying that as his client is in the final year of his contract, he could not risk playing when not 100 per cent fit.
After the narrow defeat in the second leg of the third qualifier in the Olympic stadium, where a late Scott Sinclair goal reduced the deficit after goals by Rodrigo Galo and Marko Livaja had put the home side 2-0 up, the Parkhead boss confirmed Boyata had been fit.
Rodgers, who was also without suspended defender Kristoffer Ajer, said: “Yes, we were obviously missing our two best centre-halves this evening unfortunately.
“My concentration really until I get back is only with the players that are here.
“But yes, Dedryck would have been fit to play.”
Asked if he felt frustrated on a night when defensive inadequacies proved costly, the Northern Irishman said: “Yes, of course. He has been with us on the journey now for a couple of years and helped us get to this position and of course, someone of his quality, a World Cup semi-finalist in our team, certainly would have helped.
“But he wasn’t here and we look at the performance without him and I can’t think any more than that.”
Rodgers admitted it was “very difficult” to get his head around his side’s defending which left them in a Europa League play-off spot where they will play Latvian side Spartaks Jurmala or Lithuanian side Suduva.
He said: “We conceded a soft goal against Livingston and Alashkert and against Hearts we gave away a goal.
“We are not getting opened up and fantastic goals scored against us, it is concentration and basic defending.
“So it is hard to get your head around it.
“But we will go away and work with the players we have, try to improve and make them better.
“I always say you shouldn’t have to lose to learn but when you do lose you have to learn so that is our message and we get back to the training field and try to improve.”
AEK Athens boss Marinos Ouzounidis admitted to some nerves in the final minutes and when Jozo Simunovic almost levelled in added time.
He said: “Being able to qualify in a stress-free way is impossible.
“If you want to knock out Celtic and remain cool and relaxed is impossible.
“Celtic is a great club, we have been scouting them for a long time and as far we are concerned we tried to reduce the number of good build-ups”.