The winger was substituted for Gareth Barry while City were trailing by a goal in their Champions League encounter with Spanish outfit Villarreal.
After the switch, the North West side went on to win 2-1 at the Etihad Stadium courtesy of an own goal and last-minute effort from Sergio Aguero.
Despite his removal from the field, Mancini insists that Johnson bears no grudges over the decision.
"Adam played very well but at that moment I had to do a tactical substitution," Sky Sports News quotes Mancini as saying.
"I spoke with him [afterwards] and he understood this. Sometimes every manager decides to make a substitution. Unfortunately some player has to leave the pitch."
The current Premier League leaders take on second-placed Manchester United at Old Trafford this Sunday.