Celtic lost 3-2 on aggregate to AEK Athens to miss out on a place in the play-off round of UEFA's lucrative continental club competition.
The centre-back's agent revealed this week that Celtic received offers for Boyata, including from Fulham and Fenerbahce, but he hit out at the Scottish side for rejecting them and not offering a new contract.
Rodgers insists Boyata is physically able to feature for the team, but the defender, who made three appearances for Belgium at the World Cup, did not make himself available for the game as speculation over a potential move away from Celtic Park increases.
"He was fit," Rodgers said of the 27-year-old.
"We were missing our two best centre halves, unfortunately. My concentration until I get back is only with the players who were here. But yeah, Dedryck would have been fit to play.
"Is that frustrating? Yeah because he's been with us over the course of our journey for a couple of years.
"We got to this position and were without someone of his quality. Having a World Cup semi-finalist in our team would certainly have helped.
"But he wasn't here."
Earlier, Boyata released a video on Instagram showing him receiving treatment, accompanied by a caption saying: "Unfortunately I could not play tomorrow because I'm not yet 100% operational."