The Indian Express won the Sony Ericsson Open after beating Max Mirnyi and Daniel Nestor 6-7(5), 6-2, 10-5 in the summit clash.
Paes and Bhupathi now have 2630 points, 250 more than the Bryan brothers.
Individually, Bhupathi is still at number five and Paes at number seven in the ATP doubles ranking.
In the singles rankings, Somdev Devvarman further improved his position to 71, a gain of two places, after making a third round appearance at Miami Masters.
Rohan Bopanna who was made remarkable stride in doubles is static at 15th but as a pair he and Pakistan`s Aisam-ul Haq Qureshi are now eighth improving from their 10th slot.
Sania Mirza also improved his position in top-100 as she moved to 90 from 99 in WTA singles chart.
Sania had earned 80 ranking points by reaching the second round at Miami Premier event after qualifying for the main draw.
In the doubles, she is static at number 33.