The American looked assured in convincingly clinching the first set but then appeared troubled at the start of the second by the back injury which hindered her semi-final win.
Jankovic capitalised with a break of serve to go 2-1 up, but Williams responded by reeling off the next five straight games to prevail in one hour 28 minutes.
"I'm really excited - I didn't think I'd win this tournament starting out, so I'm really happy to be here holding the trophy,'' Williams said on court after capturing her 10th title of 2013. She is the first player to do that since Justine Henin in 2007.
"Congratulations to Jelena for such a great tournament as well.
"I really love tennis so much and it's fans like the ones here in China who are so exciting to come to. The fans make me want to play, and they're so great here, so coming here is such a great opportunity.''
Jankovic acknowledged she had been well beaten by the 17-time major singles winner.
"Serena was just too good today, and big congratulations to her,'' she said.