Suicide attempt brought some supporters onto the streets
Mr Stojiljkovic - who headed the police under former President Slobodan Milosevic - shot himself in front of the federal parliament just hours after its members voted to allow the extradition of suspects to The Hague tribunal.
Yugoslav President Vojislav Kostunica described the suicide as a "tragic event" and said it was a "warning to the international community that constantly sets conditions, pressures us and dictates behaviour".
The co-operation law was passed after the United States froze its aid to Yugoslavia because of delays in handing over war crimes suspects.
But State Department spokesman Philip Reeker said Washington would wait for "urgent and effective action" before deciding whether to free up the billions of dollars of funds.
'Puppet authorities'
Mr Stojiljkovic is reported to be in a deep coma after an emergency operation by a team of neurosurgeons.
Still a member of the federal parliament, he left an angry suicide note, accusing the parliament of betrayal.
It was read out by the Radical Party legislator Aleksandar Vucic in front of the parliament.
"By this act I, as a deputy of the federal parliament, express my protest against all members of the puppet authorities," said the note.
He singled out for blame the Serbian Prime Minister, Zoran Djinjdic, and Yugoslav President Vojislav Kostunica, as well as other members of the coalition which took over following the overthrow of the Milosevic regime.
"I accuse them of destroying Yugoslavia with the assistance of our greatest foreign enemy... for ruthless violation of the constitution and laws of this country, the policy of treason and capitulation, ruin and suffocating of our national dignity," the note read.
"Patriotic citizens of this country will know how to avenge me," Mr Stojiljkovic wrote.
'No surrender'
Mr Milosevic's Socialist Party said Mr Stojiljkovic was the "first victim" of the law legalising "the hunt for Serb patriots and heroes of the war against Nato aggressors and Albanian terrorists" in Kosovo.
The party has called protests across the country, but a protest in Belgrade on Friday drew only a few dozen supporters.
The BBC's Alix Kroeger in Belgrade says Mr Stojiljkovic's attempted suicide has come as a shock, but it is not enough to bring many people out onto the streets.
Mr Stojiljkovic is one of four senior officials accused alongside Mr Milosevic for alleged war crimes during the Yugoslav military campaign in Kosovo.
During his time as interior minister, from 1998 to 1999, police units are alleged to have committed atrocities against ethnic Albanians in Kosovo.
He pledged never to surrender to the tribunal.
But the law passed by parliament on Thursday allows for the handing over of about 20 suspects, including Mr Stojiljkovic.
Yugoslav Interior Minister Zoran Zivkovic said earlier that the first extraditions could take place very soon - with all the suspects being transferred to The Hague by 1 May.