Federer did not drop a set on his way to the final, with his run including a 6-3 6-1 win over Rafael Nadal's conqueror Alexandr Dolgopolov in the last four.
MORE: Novak Djokovic fights back to claim BNP Paribas Open | Gallery - BNP Paribas Open Final
The Swiss also took the first set in Sunday's final against Novak Djokovic before the Serb fought back to win 3-6 6-3 7-6 (7-3).
However, Federer's return to the top five was assured after he made it to the final.
America's John Isner is the other major mover in the men's rankings, moving into the top 10 for the first time since September 2012 courtesy of reaching the last four at Indian Wells.
Flavia Pennetta's victory in the women's draw saw her climb nine places in the rankings to world number 12, giving Italy three players in the top 20.
Simona Halep, a semi-finalist in Indian Wells, has become the highest-ranked Romanian player in the history of the WTA.
The 22-year-old has risen two places to world number five, having been on an upward curve since the start of 2013.
Caroline Wozniacki's defeat in the fourth round to Jelena Jankovic has seen her fall six places to world number 18.