Novak advanced past the Argentine 4-6, 6-4, 6-4 in two hours and 38 minutes to move to 12-4 in their ATP Head2Head series.
The top seed retired at 3-6 in his quarter-final match against Feliciano Lopez at the 2016 Dubai Duty Free Tennis Championships on Thursday.
Novak cruised into the second round of the Dubai Duty Free Tennis Championships with a 6-1, 6-2 win over world no.41 Tommy Robredo.
Novak captured his eighth ATP World Tour title of the season and 56th of his career over no.3 seed Rafael Nadal 6-2, 6-2, in the final of the China Open on Sunday.
Djokovic improved to a 28-0 lifetime mark at the China Open as he dismissed no.4 seed David Ferrer 6-2, 6-3 in semi-finals on Saturday.