The Spain striker came on for Brazilian Oscar at halftime but lasted a matter of minutes before he forlornly trudged off the field.
Costa was unable to join the Spain squad for the recent international break after having to limp off in Chelsea's previous game at Hull City and manager Jose Mourinho admitted he took a risk by bringing him on against Stoke.
"The player has trained for the last two days at 100 percent," Mourinho told reporters after an Eden Hazard penalty and a goal from Costa's replacement Loic Remy took his side another step closer to the Premier League title.
"The medical department was convinced he was ready, the player was convinced he was ready, not for 90 minutes but to help the team.
"Sometimes as a manager I have to risk tactically, the medical department have to do the same if they want to be a top medical team. The safe medical department cannot work with me," added Mourinho.
"The medical department that says an injury of two weeks needs one month or two months cannot work with me. Safe people, people with fear, people afraid to risk, cannot work with me but my medical department is fantastic.
"Today between them, the player and me things didn't happen in the best way but ... that's football."
Chelsea, who also stuttered to a 3-2 win over Hull, again huffed and puffed their way to victory on Saturday and Mourinho was relieved to pick up maximum points.
"We didn't play better because the opponents made a very good defensive performance," said the Portuguese.
"We didn't play better because when we had a 1-0 advantage, instead of going on from that moment to build another kind of performance with more confidence and more stability, we conceded immediately a goal.
"The good goalkeeper of the game was Asmir Begovic, not Thibaut Courtois. Stoke had unbelievable efficiency but they had only two shots on goal so the game was difficult but the important thing was the three points.
"At lunchtime we needed six victories and one draw (to win the title) and now at dinner time it's five victories and one draw."
(Editing by Ed Osmond)
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