Jung was regularly in news for his power tussle with Arvind Kejriwal since the latter was elected chief minister of Delhi.
Kejriwal had often accused Jung of working at the behest of the Centre.
The Delhi CM had accused Jung of "supporting the BJP" to "cripple" Delhi. However, Kejriwal was "surprised" by Jung's exit and wished him well for his future endeavours.
Jung did "very good work" in the capital despite their bitter turf war, Deputy Chief Minister Manish Sisodia said.
"Despite the bitter-sweet experiences (with the Lt Governor), I can say that we did very good work for Delhi along with Jung," the Aam Aadmi Party leader tweeted.
"All the best for the future," Sisodia added, shortly after Jung resigned as the Lt Governor of Delhi.
Sources say former home secretary Anil Baijal is likely to replace Jung.
(ALSO READ: 5 things to know about Anil Baijal who is tipped to replace Najeeb Jung )
Jung had one and a half years of service still left. Sources say he took this decision due to personal reasons and was considering it for a long time.
In his resignation letter, he thanked Prime Minister for all the help and cooperation he received during his tenure as the Lt. Governor of Delhi.
Jung also thanked the people of Delhi for all their support and affection, especially during the one year’s President Rule in Delhi, when he got unstinted support from them and which in turn helped run the administration in Delhi smoothly and effortlessly.
He also thanked Chief Minister of Delhi for his association in the last two years.
Jung said he would be returning back to his first love, which is, academics.
Jung became the Lt Governor on July 9, 2013 when a Congress-led coalition was in office. The Modi government retained him even as it replaced most Governors in the states.
A former IAS officer from the Madhya Pradesh cadre and a former Vice Chancellor of Jamia Millia Islamia in New Delhi, Jung gave no reason for his sudden decision to step down.
Jung's tenure was marked by a sharp escalation in tensions between his office, which reported to the central government, and the Aam Aadmi Party government of Kejriwal.
(With agency inputs)