With a total of 524 points, the Australian is 127 points clear of Safin with Britain's Tim Henman, who lost to Hewitt in the Wimbledon semi-final, lying in third.
Henman has jumped four places on the back of his Wimbledon run.
Wimbledon runner-up David Nalbandian of Argentina has moved up to 11th place.
At the end of the season, the top eight in the Champions Race qualify for the Masters final in Shanghai.
In the women's WTA rankings, Serena Williams' Wimbledon triumph has pushed her ahead of older sister Venus to the top of the chart.
Jennifer Capriati retains third spot, just ahead of Monica Seles.
ATP top 10
1 Lleyton Hewitt (Aus) 524 pts
2 Marat Safin (Rus) 397
3 Tim Henman (Gbr) 378
4 Albert Costa (Spa) 340
5 Andre Agassi (USA) 332
6 Roger Federer (Swi) 324
7 Thomas Johansson (Swe) 304
8 Juan Carlos Ferrero (Spa) 287
9 Tommy Haas (Ger) 273
10 Jiri Novak (Cze) 261
WTA top 10
1 Serena Williams (USA) 5742pts
2 Venus Williams (USA) 4917
3 Jennifer Capriati (USA) 3947
4 Monica Seles (USA) 3906
5 Kim Clijsters (Bel) 3168
6 Jelena Dokic (Yug) 3076
7 Justine Henin (Bel) 3005
8 Martina Hingis (Swi) 2814
9 Lindsay Davenport (USA) 2637
10 Amelie Mauresmo (Fra) 2285