The Serbian, who has struggled with injuries in the last few months, completed a 6-3 6-4 triumph in one hour and 22 minutes in the French capital.
It took three games for Djokovic to create a break point, but he comfortably converted it to take a 4-2 lead in the opening set.
Muller managed to save two break points, but it was not enough to keep the 12-time Grand Slam champion at bay as Djokovic took a one-set lead in 35 minutes.
Djokovic almost suffered a wobble in the second set when Muller had a break point in his hands, but the top-ranked player managed to hold before breaking serve later in the contest and winning the match.
The 29-year-old will face Grigor Dimitrov in the next round of the competition.