Kirilenko was poised to claim the first set, being 40-0 ahead with the score at 5-4 in her favour, but after missing three set points, Williams stepped up a gear to overturn the scoreline.
The top seed was also forced to come from behind in the second set, with Kirilenko, a former winner in Beijing in 2005, leading at 4-3. But Williams broke back Kirilenko's serve before closing in on victory in the third-round match.
It was the second unconvincing victory in Beijing for Williams, who only showed rare moments of her trademark power-play when she overcame Italian Francesca Schiavone 6-4, 7-5 in her second-round match.
In the quarter-finals, Williams will play either Sloane Stephens or Caroline Wozniacki, who clash at Beijing's National Tennis Centre on Thursday evening.
Eighth seed Jelana Jankovic ruthlessly disposed of Spaniard Carla Suarez Navarro in her third-round match, with the Serb taking both sets 6-0, 6-0.
In the men's tournament, sixth seed Stanislas Warwinka was dumped out by American Sam Querrey 6-3, 7-6(7/2) in their second-round match.
The China Open will reach its climax on October 6.