The ruling ANC and opposition partis welcomed the decision, which followed a two-and-half day retreat by the commission on Robben Island.
Deputy President Thabo Mbeki was among the 37 leaders granted amnesty by the TRC's amnesty committee, sparking accusations that the legislation convening the TRC was being bent in favour of the ANC.
The acts for which the ANC leaders were being indemnified for were not specified, neither did the individuals appear before the amnesty committee.
Truth commission chairman Archbishop Desmond Tutu made the announcement to refer the matter to court at a news conference in Cape Town.
He said the TRC would as a matter of urgency approach the High Court to seek a declaratory order, or such other relief as counsel may advise. He said the decision was unanimous.
The move, he said, was to ascertain whether or not the decision made by the amnesty committee conformed with the commission's governing legislation.
"Because our Act gave the committee absolute autonony in its deliberations, the only option we as a commission have in this matter is to act as we have done, and go to court," Tutu said.
"We remain confident that this process will quickly and effectively resolve the current impasse.
"We have also had close discussions with the amnesty committee, several of whose members were present at the Robben Island meeting."
Tutu denied reports of serious dissension or disagreement among commissioners on the matter.
TRC deputy chairman Dr Alex Boraine said the TRC was satisfied all provisions had been taken into account regarding the amnesty granted to Archbishop Tutu's son, Trevor, for his 1989 bomb threat at East London airport.
The National Party, Democratic Party and the Freedom Front welcomed TRC's decision to go to court.
"The TRC's decision confirms the National Party's viewpoint that the 'blanket' amnesty granted to 37 ANC leaders (was) illegal," party leader Marthinus van Schalkwyk said in a statement issued in Cape Town.
He said the TRC bowed to pressure from his party and others after initially defending the amnesty.
"If the court application is not unambiguous in seeking relief to set aside the 'blanket' amnesty, the National Party will have no option but to enter as a party," Van Schalkwyk said.
"The application must have as its main focus the restoration of the principle of equality before the law. We cannot have a situation where there is one set of rules for the ANC, and another set of rules for other South Africans."
The Democratic Party's TRC spokeswoman, Dene Smuts, said the DP would approach the commission for discussions on the matter. She said party had decided to join forces with victims of ANC acts, and to take the amnesty committee's decision on review.
The Freedom Front said it hoped the TRC had learnt its lesson and would in future act objectively.
"With this decision, the TRC is acknowledging that it had acted in favour of the ANC," a statement said.
The Pan Africanist Congress said the court application was a waste of taxpayers' money.
The ANC said it would abide by the court ruling, and hoped it would end controversy over the matter.
"We hope that the courts will lay the matter to rest once and for all, particularly in the light of concerted efforts from certain political quarters to undermine the integrity of the TRC, and thereby bring the entire truth and reconciliation process into disrepute," said Ronnie Mamoepa, the party's national spokesman.
"The ANC commits itself to respect and abide by whatever findings the court may arrive at," he said.
Tutu told the news conference the commission had carefully considered its own concerns and the clear public interest that existed.
Tutu reaffirmed the TRC's confidence in the amnesty committee.