After a division was called for by some members, 147 members voted in favour of the Bill and 42 against.
The Lok Sabha has already passed the Bill, under which the government can designate individuals as terrorists if they commit or participate in acts of terrorism, prepare for acts of terror, promote terrorism or are otherwise involved in terrorism.
Replying to the debate on the Bill, Home Minister Amit Shah said it was important to name terrorists individually as it had been seen that when terrorist organisations were banned, the terrorists floated another outfit.
Many opposition parties opposed this provision, saying this could be misused.
Congress leader P. Chidambaram said that tagging an organization as terrorist was different from naming an individual. He stressed that the provision violated individual liberty.
"Let me caution you, the government, that it will be struck down. Instead of listening to us here and making the necessary correction, you are forcing us to go about a kilometre away to another building (Supreme Court) and (ask) another set of individuals to strike it down. How does it raise the esteem of Parliament?
"We are doing something which is hopelessly unconstitutional," the former Union Minister said, adding the Bill should be sent to a Select Committee.
( With inputs from IANS )