The top-ranked Djokovic is attempting to match Roger Federer's record of six titles at the season-ending event for the top eight players in the world.
Djokovic was again almost perfect on his serve, although Rublev managed to break him in the opening game. Djokovic broke twice in each set and won the match with his 12th ace.
Djokovic is now 2-0 in the Green Group. He beat Casper Ruud in his opening group match.
Ruud will face Cameron Norrie later Wednesday. Norrie was called in as the second alternate after 2018 champion Stefanos Tsitsipas was forced to withdraw with an injury. Matteo Berrettini was replaced by Jannik Sinner on Tuesday.