Ganguly was accompanied by orthopaedic specialist Dr Kalyan Mukherjee who had been treating the cricketer since his return to the city midway into the tour.
Ganguly, who left via a Sahara Airlines flight, from the NSC Bose International Airport in Kolkata is expected to catch a connecting flight to Lahore from Delhi later in the day.
"He is completely fit and I don't see any reason why he cannot play the third Test," Mukherjee said. The third and final Test in the ongoing series is scheduled to begin at Rawalpinidi from April 13.
On Tuesday, Ganguly was issued a fitness certificate by Mukherjee following which the Board of Control for Cricket in India's (BCCI) sent the player's medical record to Dr Anant Joshi, the Board's chief medical consultant. The BCCI gave the nod for Ganguly to rejoin the team after clearance from Joshi.