The Portuguese coach, who celebrated Champions League victory last season with Inter Milan, saw his new side have to work hard for victory.
The two-goal triumph came via a goal in each half from Argentine hitman Gonzalo Higuain though the first may be credited as an own goal.
"We played very well, we pressed a lot and did not let them play as they like. One day some poor team will pay for all these chances we missed," said Mourinho.
"It was a game of boys against boys because Madrid has a team of boys. If you take out [Iker] Casillas and [Ricardo] Carvalho then it's a team of all boys, less so Xabi Alonso who is the father.
"I'm not concerned that Cristiano has not scored. The goals will come. He has worked very well and can score a couple of goals in any game. You must let Cristiano and Higuain be, many coaches would like to have these forwards. Goals will come."