The Cameroon international was forced off shortly after the interval at Old Trafford, having started alongside Kobbie Mainoo in midfield for the first time.
Baleba had burst forward early in the second half and appeared poised to create a dangerous opportunity when he suddenly pulled up in discomfort. He was unable to continue, with Youri Tielemans introduced in his place.
Carrick confirmed after the match that the problem was to Baleba's hamstring, although the club would need to carry out further assessments before establishing the severity.
“I haven’t got any more news on Carlos at this stage but it’s his hamstring,” the United head coach said.
“We’ll have to assess what that looks like but, initially, it doesn’t look great.”
The injury came at a difficult moment for United, who had gone into half-time trailing 2-0 after goals from Matías Soulé and Donyell Malen. Bruno Fernandes converted a penalty before Matheus Cunha scored twice to complete a remarkable comeback.
Tielemans made a positive contribution after replacing Baleba, earning praise from Carrick for the way he handled the circumstances.
“I thought Youri stepped into the game and showed what he’s about, his personality and character stepping into the team,” Carrick said.
“He’s a top human being, I love having him around for everything that he brings.”
The Belgian's performance could strengthen his case for a starting place when Manchester United face Aston Villa at Old Trafford on Sunday.
Baleba's absence would be a setback for Carrick, particularly after the midfielder had been paired with Mainoo from the start for the first time. United will now wait for the results of further examinations before knowing whether he will be available for the coming fixtures.