As Standard Sport reported ahead of Chelsa's 2-1 victory at the bet265 Stadium, Hazard remained in London while the squad travelled north on Friday.
Hazard is expected to withdraw from international duty for Belgium's forthcoming games against Greece and Russia.
And Conte revealed after the game: "In the last training he felt a bit of a problem in his calf, for this reason I decided not to risk him.
"That is why he didn't play today."
Gary Cahill, who had earlier given away a penalty, smashed in late on to hand Chelsea victory at a venue where a November loss last season had seen them slip 16th.
Willian had given them the lead here with a free-kick only for the Potters to draw level through Jonathan Walters' penalty
"I am pleased. To play Stoke at this point of the season, you have to be prepared mentally and physically. For this reason, we won today," added Conte.
"We need to take 21 points for the title win. There are 10 games to go, today was a great win, a good signal, but it is important to continue with the same commitment and work rate as a team."