As a result, Nadal left the ousted Swiss tantalisingly short of equalling Pete Sampras's record time as World No 1.
Federer, beaten in the quarter-finals by Sweden's Robin Soderling at Roland Garros last Tuesday, dropped to second just one week short of matching the American's record total of 286 weeks as No 1.
Nadal last held the number one slot on June 29, last year.
The 24-year-old Spaniard's 6-4, 6-2, 6-4 defeat of Soderling on Sunday handed him a fifth French Open title and also made him the first player to qualify for the season-ending ATP World Tour finals in London in November.
Soderling moved up one place in the rankings to a career-high sixth while Argentina's Juan Martin del Potro, who missed the French Open while he recovers from wrist surgery, dropped to eighth.
Nadal batters Soderling for 5th French Open crown
Bopanna-Qureshi in semis of Morocco ATP event
Argentina name Del Potro for singles
Robin Soderling top seed at Chennai open
Del Potro knocks out top seed Ferrer