The number four seed broke Azarenka early in the first set to race into a 3-0 lead, before the Belarusian broke back in the fifth game of the set to make it 3-2.
Li hit back immediately, however, breaking Azarenka twice on her way to winning the next three games and seeing out a 6-2 victory.
It was more of the same in the second set from the in-form Chinese player as she won the opening five games, including breaking the number two seed with back-to-back love games.
Azarenka did manage to avoid a whitewash by winning the penultimate game, but Li served out to take the set 6-1 and secure her spot at the top of the group.
Li had already booked her place in the semi-finals of the tournament, but the result means that Azarenka will no longer join her in the final four.