The Swiss maestro withdrew from the ATP World Tour Finals decider due to a back injury, putting his participation in Switzerland's Davis Cup tie against France in doubt.
Djokovic, who claimed the title in London for the third straight year, said there was no way Federer decided to skip their final just to be able to compete in Lille starting Friday.
The Serbian said there was a "question mark" over Federer's appearance in the Davis Cup.
"He [Federer] is one of those players that would compete and would always fight if he can," Djokovic told a news conference.
"He has had, what, three retirements in his entire career.
"I don't think he was calculating and trying to save his body for Davis Cup final. I'm sure that that wasn't the case.
"This is probably one of the biggest matches of the year for him, as well as for me. You know, you have grand slams that are the pinnacle of the sport, and you have World Tour Finals.
"Then you have of course Davis Cup, [ATP] 1000 events, there are many tournaments, but you know this is probably the biggest match of the season next to the final of a grand slam.
"I'm sure if he could have, he would be on the court. I mean, I spoke to him. Also he doesn't know. It's a question mark for the Davis Cup final, as well."