Israel's UN ambassador, Yehuda Lancry. said Israeli lawyers who had contributed to formulating the court's statutes "had in mind and in heart the memories of the Holocaust - the greatest and most heinous crime against mankind."
The US move came only hours before the deadline after which no more signatures will be accepted. Israel and Iran followed suit.
President Bill Clinton said he had endorsed the international court in order "to reaffirm our strong support for international accountability and for bringing to justice perpetrators of genocide, war crimes and crimes against humanity".
But observers say other reasons include maintaining US leverage in defining the court's parameters and trying to set the agenda for his successor and the next Congress.
Republican opposition
Conservatives in the US have opposed moves to set up the court for fear that it might encroach upon US national sovereignty.
Senator Jesse Helms, the influential Republican chairman of the Senate Foreign Relations Committee, described Mr Clinton's move as "a blatant action by a lame-duck president to tie the hands of his successor."
The Senate must ratify the treaty for Mr Clinton's signature to be valid.
The court will act much like the two temporary war crimes tribunals currently investigating the 1994 Rwandan genocide and the Yugoslav conflicts.
Supporters of the project hope that, because the tribunal will be a permanent body, it will be able to deliver swifter justice than an ad-hoc one, and thereby act as a greater deterrent.
Hold-outs sign
Israel signed the treaty a few hours after the US did.
Israel's UN ambassador, Yehuda Lancry.
said Israeli lawyers who had contributed to formulating the court's statutes "had in mind
and in heart the memories of the Holocaust - the greatest and most heinous crime against mankind."
The Israelis had been concerned that under the new court's jurisdiction, Jewish settlers in the occupied territories could be charged with war crimes.
Iran also signed the treaty shortly before the deadline.
Reservations
Mr Clinton said he still had reservations about some aspects of the treaty, including the possibility that the court might not be able to exercise authority over countries that had not ratified the treaty.
The president had come under pressure from defence officials not to sign until Washington had guarantees that no US servicemen or other government officials abroad would be subject to the court's jurisdiction.
BBC correspondent Tom Carver says the move is certain to be criticised by conservatives, who fear the court could subject American citizens to politically motivated prosecutions.
Based on Nuremberg
The tribunal - which will be set up in the Netherlands and based on the principles of the Nuremberg Nazi war crime trials at the end of World War II - will come into existence automatically after 60 countries have ratified the treaty.
So far, 139 countries have signed the treaty and 27 have ratified it.
The United Kingdom, which signed the treaty in November 1998, is expected to ratify it within the next few months.