The former Arsenal midfielder was a surprise absentee from the Blaugrana starting line-up for the midweek meeting with the Rossoneri at San Siro, and also sat out Saturday night's La Liga win over Athletic Bilbao.
However, Guardiola has revealed that while Fabregas has been experiencing some pain in his lower back, he was rested for both games purely as a precautionary measure.
"Cesc had a problem in the sacrum [a large, triangular bone at the base of the spine] on Thursday," the Blaugrana boss told reporters after Saturday's 2-0 victory over Athletic.
"We've dealt with it and today he was better. So, even though we were forced to leave him out [against the Basques], he will there against Milan on Tuesday."
Barca's eagerly-awaited meeting with Milan at Camp Nou gets underway at 20.45CET, with the tie still scoreless after last Wednesday's clash at the Giuseppe Meazza.