The Indo-Czech pair had a match point at 5-4 on Bob's serve, but could not convert and the set went to the tie-breaker.
Paes and Dlouhy raced to a 5-0 lead in the tie-breaker, before Bob and Mike fought back. The Americans saved four match points at 6-2 to draw level. Finally Paes and Dlouhy wrapped it up in their sixth match point with Paes showing great reflexes at the net and putting away a volley.
The French Open doubles champion will meet the winner of the other semi-final between India's Mahesh Bhupathi and Mark Knowles of Bahamas and Andy Ram of Israel and Max Mirnyi of Belarus.
Paes, who won the title here in 2006 partnering Martin Damm, entered the US Open title round for the fifth time. He has also advanced in the mixed doubles final here with Zimbabwean Cara Black.