Their meeting began at 6.30 PM and lasted for an hour.
Jung is believed to have discussed with Jain the "personal reasons" that led to his resignation on December 22.
Chief Minister Arvind Kejriwal, his deputy Manish Sisodia and Labour Minister Gopal Rai, have already met Jung after he stepped down.
Jung and Jain have been at loggerheads over a range of issues, including outbreak of chikungunya and foreign visits by AAP ministers, during Jung's tenure as Delhi's Lt Governor.
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A day after his resignation, Jung's office said "he would be returning to academics", but did not cite any reason for his sudden decision to exit administration.
Jung has had a bitter-sweet relationship with Delhi's AAP government over matters of jurisdiction. But his decision to quit was said to have no connection to that relationship.
Jung also met Prime Minister Narendra Modi a day after resigning.