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His resignation was accepted by Rajasthan Governor and university Chancellor Kalyan Singh, officials said.
The resignation came a day before a hearing scheduled in the Rajasthan High Court on the controversial appointment of Mr Singhal, who was appointed as VC of the University in August 2015.
The Chancellor on the advice of state government has given the additional responsibility of the VC to Jaipur divisional commissioner Rajeshwar Singh, a release from the Governor House said.
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The Court had not pronounced its verdict in the case during its last hearing on January 4 and deferred it till January 9.
The double bench of the court comprising justices K S Jhaveri and Vineet Kumar Mathur had heard the PIL filed by former judge of High Court I S Israni and others challenging Mr Singhal’s appointment.
Mr Singhal had courted controversy soon after his appointment with the state unit of Congress claiming he did not fulfil the eligibility criteria for post as prescribed by the UGC in 2010 and was made the VC allegedly due to his proximity to the Rashtriya Swayamsevak Sangh.