Fernandes managed just 58 passes in total in their opening Group F win against Hungary and subsequent 4-2 defeat by Germany, and has struck just one shot on target.
Ahead of their meeting with France, Mourinho told talkSPORT: "Portugal at its highest level can beat anyone.
"But we need to play with 11 players, in these two matches Bruno Fernandes was on the pitch but not playing.
"I hope he turns up against France, because he's a player with incredible potential.
"He can pass, he can score. He can get penalties, he can score penalties, he can score free kicks. He has a lot to give, but the reality is in these two matches he was not there.
"Portugal has three fantastic attacking players, Bernardo Silva, Cristiano [Ronaldo] and [Diogo] Jota. We need that connection, but until now Bruno is not playing."