Mourinho was pictured on Hadley Common in Barnet with the France midfielder - whose has struggled for fitness since joining Spurs for Â£55million in July - along with two members of the public.
Davinson Sanchez and Ryan Sessegnon, who like Ndombele live locally, were also pictured jogging side-by-side in the same area and are thought to have come across Mourinho and Ndombele but were not involved in the session.
Official government advice during the coronavirus pandemic is that all individuals should stand at least two metres apart at all times, and exercise outdoors can only be undertaken with one other person from your own household.
Mourinho was spoken to by senior officials at the club, who were not impressed with the manager's decision.
A Spurs spokesperson said: "All of our players have been reminded to respect social distancing when exercising outdoors. We shall continue to reinforce this message."
This story has been corrected. An earlier version stated Davinson Sanchez and Ryan Sessegnon were part of Jose Mourinho's fitness session.