Djokovic sees off Cilic threat to book semi-final spot at Paris Masters
The Serbian is set to return to number one in the world rankings.
The Serbian, who will take the world number one ranking from Rafael Nadal on Monday, won 4-6 6-2 6-3 to extend his winning run to 21 matches.
The 14-time major winner, 31, lost his cool in the second set after an outburst at his own box, before breaking his racket in the third.
But Djokovic, the number two seed, remains on course to win a fifth Paris Masters title after sealing the win in two hours and 12 minutes.
Russian Karen Khachanov ran out a comfortable 6-1 6-2 winner against fourth seed Alexander Zverev in their last-eight encounter.
The world number 18, who needed just over an hour to beat Zverev, will face Dominic Thiem in the semi-finals.
Thiem, the French Open finalist, came from behind to win 4-6 6-4 6-4 against Jack Sock, who won the title in Paris last year.