The Czech 16th seed, Mensik, came through a tight third-round clash against American Ethan Quinn, with a 6-2, 7-6(5), 7-6(5) win on Saturday, but the 20-year-old said he had been carrying an injury that prevented him from facing his mentor, Djokovic.
Djokovic, the 10-time Australian Open champion, will now continue his quest for a record-extending Melbourne Park title and standalone 25th Grand Slam crown to break the tie with Margaret Court.
"This is a tough one to write," Mensik said on Instagram.
"After doing everything we could to keep going, I have to withdraw from the Australian Open due to an abdominal muscle injury that has progressed over the last matches.
"Now, it's time to recover properly."
"Even though I'm disappointed, making the fourth round here for the first time is something I will carry with me for a long time. I felt so much energy from the fans and the atmosphere in Melbourne was truly special."
Serb Djokovic was beaten by Mensik the last time the duo faced off, in the Miami Open final last year.
The fourth seed faces American Taylor Fritz or Italian Lorenzo Musetti in the quarter-finals, with a potential clash against defending champion Jannik Sinner in the semi-finals.
