Former Australian Open champion Stan Wawrinka has dropped to eighth after losing in the second round of the Indian Wells tournament while Spain's David Ferrer climbed one place to seventh.
Federer, who lost to Djokovic in the Indian Wells final on Sunday, remained in second place ahead of Spaniard Rafael Nadal.
Britain's Andy Murray is in fourth place, followed by Japan's Kei Nishikori in fifth and Canadian Milos Raonic took sixth spot.
Top ten Rankings:
1. Novak Djokovic (Serbia) 13,205
2. Roger Federer (Switzerland) 9,205
3. Rafael Nadal (Spain) 5,810
4. Andy Murray (Great Britain) 5,695
5. Kei Nishikori (Japan) 5,460
6. Milos Raonic (Canada) 5,160
7. David Ferrer (Spain) 4,580 ( 1)
8. Stan Wawrinka (Switzerland) 4,515 (-1)
9. Tomas Berdych (Czech Republic) 4,510
10. Marin Cilic (Croatia) 3,370