Nadal became the first player since American Jim Courier in 1991 in Indian Wells to win the singles and doubles titles at a Masters Series event when, with compatriot Tommy Robredo, he beat Mark Knowles and Mahesh Bhupathi 6-3, 6-3 in the doubles final.
The 21-year-old Nadal improved his personal record against Federer to 9-6 (7-1 on clay) and is undefeated on the Monte Carlo clay since a third-round loss to Argentine Guillermo Coria in 2003.
"I just tried to put pressure on his backhand when I had the chance, tried to be aggressive and tried to have a good long return," said Nadal after clinching his first title of the year.
"I am very happy, for sure. It is a very special moment for me. I played all the tournaments this year very well but I didn't play the last match of every tournament well because I lost easily in Australia, Indian Wells and Miami."