"There are still 33 points up for grabs," said Mourinho. "There is a long way to go yet. I cannot think the Scudetto is over."
Inter got first-half goals from Brazilian Adriano and Serb Dejan Stankovic and then held on against Milan, which lost Englishman David Beckham with a hamstring injury.
Milan coach Carlo Ancelotti blamed the loss on Adriano's opening goal, which he claimed should have been called off for a handball.
Adriano scored in the 28th minute when he diverted Maicon's cross with his arm into the goal. The Brazilian said the handball was unintentional.
"It's true that I touch the ball with my arm," he said, "but it was inadvertent. I wanted to score with my head, but my hand was where it usually was. For me, it was involuntary, and all who have seen it agree that it was so."
Stankovic gave Inter a 2-0 lead at the half. Brazilian Alexandre Pato scored with 20 minutes to play, but Milan could not get the equalizer.
Second-place Juventus fell nine points behind Inter when it was held to a 1-1 tie by Sampdoria at home.