The world number one claimed a 6-3 6-2 win over world number five Rublev in the first-ever meeting between the two on Thursday.
Djokovic confirmed his place as winner of the Green Group with his second consecutive victory, having also beaten Casper Ruud in straight sets in his opening match on Monday.
Despite Rublev's ranking, Djokovic dispatched his opponent in one hour and eight minutes as he raced to a 40th career ATP Finals victory and his 50th on tour this year.
The start of the match was close as the Russian broke Djokovic in the opening game, but the world number one responded in kind in the next game and eventually eased away to win the first set 6-3 as Rublev made some costly unforced errors.
The second set was decided in similar fashion, with Rublev fading as Djokovic, who faces Cameron Norrie in his last round-robin match on Friday, broke twice to comfortably claim the victory.