Djokovic, a 12-time major champion, and Stepanek announced their partnership during a joint appearance on Instagram Live on Thursday.
Said Djokovic: "So this is the new team, baby. This is my new man."
Added Stepanek: "Now it's official."
What was not immediately clear was how Stepanek and Andre Agassi, who began working with Djokovic on a part-time basis at the French Open in May, will divide their coaching duties. Djokovic split from longtime coach Marian Vajda shortly before bringing aboard Agassi, and stopped working with Boris Becker a year ago.
Djokovic hasn't competed since a loss at Wimbledon in July, citing a right elbow injury.
Stepanek retired as a player in November and turned 39 on Monday. He was ranked as high as No. 8 in singles and No. 4 in doubles and won two Grand Slam men's doubles titles. He also won a bronze medal in mixed doubles for the Czech Republic at the 2016 Rio Olympics.