The World No.1 was thoroughly extended by Azarenka before clinching her 17th grand slam crown in two hours 45 minutes of enthralling action on the Arthur Ashe Stadium Court.
Williams, who twice served for the championship in the second set, made no mistake at 5-1 in the decider, taking advantage of her second match point when her opponent from Belarus hit long.
It ended brave resistance from the second seed, who had trailed by two breaks of service in the second set before hitting back to win a tense tiebreaker 8-6.
But Serena was not to be denied her fifth U.S. Open title, opening up a double break advantage, which this time she was not to relinquish.
At 31 she is the the oldest winner of the hard court grand slam in the Open era and acknowledged just how tough a match she had been given.
“Victoria you played unbelievable,” Williams said. “What a great match and a great person. It’s an honor to play against you.” she told the crowd.
Azarenka, beaten by Williams in the final in New York for the second straight year, admitted a second defeat was hard to take.
“It’s a tough loss but being in the final against the best player, who deserves the win, it’s incredible,” Azarenka said.
“I gave it everything I had. I fought hard but well deserved. Congratulations Serena.”
Williams picked up a check for $3.6 million, including a $1 million bonus for winning events in the build up to the final slam of the season.
She is the first woman to successfully defend the title since Kim Clijsters in 2010, claiming her second grand slam of the year after winning the French Open for the second time.
Earlier, Leander Paes became the oldest man to win a grand slam title when he paired with Radek Stepanek to win the men’s doubles title.
The 40-year-old Indian and his Czech partner, the fourth seeds, beat Alexander Peya of Austria and Brazil’s Bruno Soares, the second seeds, 6-1 6-3.
Paes and Stepanek were winners of the 2012 Australian Open title and had ended the hopes of top seeds Bob and Mike Bryan, who were hoping to complete a calendar year grand slam, in the semifinals.
Paes had won the US Open title with Martin Damm in 2006 and Lukas Dlouhy in 2009 and now has eight men’s doubles trophies at the majors as well as six mixed doubles crowns.
“I think the best advice I can give to anyone for doubles is get a partner from the Czech Republic!,” Paes told the official tournament website.
“Radek helped me to get to be the oldest man to ever win a grand slam in the Open era. I thank him for that, and we are definitely not done. I’m going after 41 now, 42, and then 43.”