Varthaman started flying the MiG 21 about two weeks ago, nearly six months after sustaining injuries while ejecting from a fighter plane on February 27.
On Monday, IAF Chief Dhanoa and Abhinandan took a sortie on the MiG 21 jet from the Pathankot air base, officials said.
The 36-year-old IAF pilot was captured by the Pakistani Army on February 27. Before his jet was hit, he downed an F-16 fighter of Pakistan.
Varthaman was released on the night of March 1 by Pakistan. He was taken off flying duties because of his injuries. Varthaman was conferred the Vir Chakra, the coveted wartime gallantry medal.
The Vir Chakra is the third highest gallantry award after the Paramvir Chakra and the Mahavir Chakra.