Guardiola revealed the 25-year-old was left out purely as an injury precaution.
He said: "Bernardo had done nothing wrong, but there was some little muscular problems."
Riyad Mahrez was called into the line-up to replace Silva and had a terrific game, drawing praise from his boss over his attitude.
"Riyad called me after they [Algeria] won [the AFCON]," Guardiola told Goal. "He said, 'I need just 10 days. I want to come back soon. I want to play'.
"I like it. That's why I decide, 'Okay, I want to play him'."