The British No 2, who pulled out of two recent tournaments with a toe injury which severely hampered his US Open planning, had beaten the left- handed Carlsen in their previous two meetings but faced an uphill task after losing the first set 6-7 after going down 7-3 in the tie-break. But he bounced back in the second set, finding some rhythm to take it 6-2 and level the match against the 6ft 4in Dane.
Rusedski's powerful serve finally wore down the 26-year-old Dane's resistance and he took the final set 7-5 to progress to the next round.
Pete Sampras and Martina Hingis will be the top seeds in New York next week. Sampras's long-time rival Andre Agassi has been seeded second following Sunday's victory over the Russian Yevgeny Kafelnikov at the Legg Mason Classic in Washington which elevated the Las Vegan to world No 2. Britain's Tim Henman is seeded sixth.
The two-time defending men's champion, Patrick Rafter of Australia, will be the fourth seed behind Kafelnikov, the Australian Open champion.
Carlos Moya has been seeded eighth, but his preparations took a knock when he tumbled out of the Hamlet Cup in New York at the first hurdle on Monday. The unseeded Brazilian Fernando Meligeni defeated Moya 6-7, 7-6, 6-3.
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