Li, currently World number 3, had entered the final beating world champion compatriot Wang Yihan in the semifinal.
Li had a 4-1 career record over Saina, but today was Saina's day.
Despite losing the first game tamely, Saina, who is currently world number 5, made an amazing comeback, saving two match points in the second game, and winning both the second and third games with close margins to win the title.
Jakarta is Sain's favourite ground. She won the Indonesia Open title here in 2009 and 2010. saina had demolished Ji Hyun Sung of Korea in straight games in the semifinal on Saturday to set up the title clash.