The Bahamian-Canadian double act had lost their three previous Grand Slam doubles finals but ended that run by beating the French pair of Michael Llodra and Fabrice Santoro 7-6 6-3.
"We put whatever is in the past behind us. I know three is a charm, but I was hoping fourth time would be a charm as well," said Knowles.
"We knew we had to play a good match and try to forget about all the other stuff."
The pair, whose 1995 Australian Open final defeat was followed by losses in the 1998 French Open final and the 1998 US Open final, teamed up at the start of the year after a two-year split.
Nestor joined forces with fellow Canadian Sebastien Laureau in 2000 to win gold at the Sydney Olympics.
In 2001, he played with Sandon Stolle but decided to approach Knowles again this year.
"I think we have a bit of magic and just thought we could become a really good team again," said Nestor.
Knowles is preparing for a hero's welcome in the Bahamas.
"It will be like Goran Ivanisevic returning to Croatia after winning Wimbledon," he said.
"I have the advantage of being a big fish in a very small pool in the Bahamas. This will be really big news there.
"When we won the semi-final, the press guys called and said they were going to keep the newspapers open until the result of the final.
"I tried not to think about that but it did add a little pressure."