A moderating force, although Serb heads expressed fears his death may create a vacuum among his ethnic Albanians.
Mr Rugova died at his home in the Kosovo capital, Pristina. His funeral has been set for Wednesday and five days of mourning announced.
Regarded as a moderate proponent of independence, he came to prominence in the 1990s as leader of the resistance against Serbian rule.
His place at the table will be missed, the UN envoy overseeing the talks, Finnish President Martti Ahtisaari, said: "I'm certain that President Rugova would have liked to see that we will proceed with the status negotiations."
Kosovo has been under UN administration since 1999 when a Nato bombing campaign stopped Serb forces expelling ethnic Albanians during a separatist war.
Mr Rugova's non-violent campaign for independence earned him high regard in the international community.
When Serbian President Slobodan Milosevic revoked Kosovo's autonomy in 1989, Mr Rugova founded the Democratic League of Kosovo (LDK), which created its own system of hospitals, schools and taxation, boycotting the Serbian administration.
It gave him "father of the nation" status among some Kosovo Albanians.
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