Djokovic confirmed Stepanek had joined his coaching team on Instagram last week and that appointment means Agassi will only be with the Serb at the major events.
The former world number one missed the latter half of this year with an elbow injury but is expected to be fit for the Australian Open.
Agassi should be with the six-time champion in Melbourne but beyond that the pair may not work together again until the build up to the French Open at the end of May.
“Andre will only travel to major tournaments,” said Stepanek.
“I’ll be working with Novak on a day-to-day basis.
“We’ve all talked to each other and the feeling is right away that we’re in the same tune.
“The most important thing is that we understand each other and know what we really want.”