The questioning of Tharoor by a five-member SIT team took place at the Anti Auto Theft Squad (AATS) office in Vasant Vihar in South Delhi.
Delhi Police had earlier examined the former Union minister on January 19.
Tharoor was seen leaving with his lawyer after the questioning tonight.
He is likely to leave for Thiruvananthapuram tomorrow.
Tharoor's interrogation came on a day when Sunanda's viscera sample was sent to a FBI laboratory in the US for further probe.
According to police sources, Tharoor sought a break in the questioning during the day on the ground he had to attend an event at the India Habitat Centre here.
Tharoor's domestic help Bajrangi and Narayan Singh, his common friend Sanjay Diwan, his PS Praveen Kumar and Rajat Mohan (cardiologist of Sir Ganga Ram Hospital) were questioned along with him earlier in the day. Besides, they were also separately quizzed.
There were allegations that he had "misused" his office to ensure that Rs 70 crore, which was equivalent to 19 per cent equity in IPL Kochi franchise Rendezvous Sports, was paid to Sunanda, a charge denied by him.
Sources also said that a top senior police official, who is a member of SIT, left for the US to give the sample of Sunanda's viscera to Federal Bureau of Investigation (FBI).
Tharoor first reached Sarojini Nagar police station and was later taken to the office of AATS around 11.30 AM where he was questioned by the SIT team.
The SIT team, headed by Deputy Commissioner of Police (DCP) Prem Nath and comprising Additional DCP P S Kushwaha and three senior officers asked Tharoor about his relations with Sunanda and some other aspects.
DCP Mangesh Kashyap from the Economic Offences Wing (EOW), who was also part of the team, asked some questions to Tharoor about the now defunct IPL Kochi franchise.
Police Commissioner B S Bassi said, "We called six witnesses today in the second round of questioning into the case. The SIT confronted them and once again recorded their statements.
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