With her latest victory, the top-seeded American secured her 36th career title and third this season.
The former Wimbledon champion had not lost a set this week before Sunday's final. She struggled because, in the disastrous second set, her serve was broken three times, and she double-faulted five times.
"Sometimes in the match, I was a little disappointed with the errors I was making, and it made it a lot tougher for me," Williams admitted. "But at the end, I guess in the last few games, I started to play much better."
The fourth-seeded Kirilenko, last week's winner at the Sunfeast Open in Kolkata, India, had won her last nine matches dating back to a third-round loss at the U.S. Open.