"I am deeply saddened at your loss. May God give you strength in this hour of grief", Singh told Tharoor.
Sunanda Pushkar, who was upset over an alleged extra-marital affair between Tharoor and a Pakistani journalist, was found dead in a five-star hotel room.
Police said they did not suspect any foul play in Sunanda's death and it may be a case of suicide.
The body of 52-year-old Pushkar, a woman entrepreneur who married Tharoor in August 2010, was found in mysterious circumstances in luxury Leela Palace hotel in South Delhi, top police sources said.