The world No.1 crushed Pouille 6-1 6-2 in just 50 minutes in a superb display at the ATP 500 tournament in Tokyo.
Djokovic had won his previous two meetings with the Frenchman in straight sets, including in the Australian Open semi-finals this year, and was in complete control from the outset in windy conditions.
The 16-time grand slam champion won eight of the first nine points, breaking when Pouille netted a volley in the second game.
Pouille could win only two of the first 14 points of the match, losing the opening set in just over 20 minutes.
Djokovic, who is playing his first tournament since retiring in the US Open fourth round because of a shoulder injury, was flawless and Pouille had no answers as the Serbian rolled out to a 4-0 lead in the second set.
After his third straight-sets win of the week, Djokovic will face either David Goffin or Hyeon Chung in the semi-finals.