Gerard Pique and Pedro both struck for Barca before the half-hour mark to put the game out of Inter's reach.
“Barcelona have a structure of football and Pedro filled in for [Zlatan] Ibrahimovic. We, however, missed [Wesley] Sneijder a lot more than they missed their players,” Mourinho told Sky Italia television.
“In terms of quality with the ball, Sneijder thinks faster than the others, knows how to play under pressure and is from a football school where moving the ball quickly is second nature.
“After a game lost clearly I don't like to talk about Sneijder's absence nor the clear penalty, as they deserved the win. Barca played much better in the first half, the second was more balanced and we should've had a clear penalty which at 2-1 would've given us a real boost.
“Having said that, Barcelona are a better side, they played better tonight and deserved the win. We can still qualify and the result is in our hands.
“We are a long way from matching Barcelona in terms of individual quality, the quality of the team and the football system. If we face them in a one or two-match knockout then we can win and anything can happen, but looking at the two teams, they are better.”
Mourinho added: “I expected the team to be less afraid of playing and with more passion. It's true Barca have a higher tempo and are quick to put the pressure on, while we all know how quickly they move when going forward.
“If you tell me we'll face Barcelona in the semi-final, then I'm more than happy, as that means we have got that far and anything can happen. However, if you ask which side is better, I can very objectively say Barcelona.
“My players work hard and I can never doubt their work ethic. In the first half we couldn't string two passes together, even losing the ball on our own throw-in."