After she blew through the first set 6-1 by using three service breaks, the former world No. 1 lost the second set 5-7. Williams then won the match by taking the third set 6-3 on her seventh championship point.
Williams got so frustrated in the third set she drew a racket abuse penalty. It came when Jankovic rallied to 3-5 after Williams started the set with a 5-0 lead.
Williams, the tournament's eighth seed and its defending champion, earned her 30th title in 41 career finals.
Jankovic, the fourth seed, made a determined effort while fighting a head cold.
"I've beaten her many times, so I know how to play against her and know what to expect from her," Jankovic had told The Miami Herald Friday.