When the Yugoslav army abandoned Kosovo under fire from Nato's air onslaught, it was the KLA fighters who appeared ready to reap the political benefit.
His party defeated that of Hashim Thaci, former leader of the Kosovo Liberation Army (KLA) - the guerrillas who led the 1998 rebellion against Serbian rule.
When the Yugoslav army abandoned Kosovo under fire from Nato's air onslaught, it was the KLA fighters who appeared ready to reap the political benefit.
Mr Rugova's decade-long policy of passive resistance looked threadbare - but now he is back with a vengeance.
Pacifism discredited
A French-educated intellectual always seen in a silk scarf, Mr Rugova had long argued that open rebellion against Serbian domination would prove disastrous.
At a time when Serb forces had driven hundreds of thousands of people from their homes in Croatia and Bosnia, he feared the same could happen to Kosovo's ethnic Albanian population.
Mr Rugova's popularity was further dented by his appearance in televised talks with the now ousted Yugoslav President Slobodan Milosevic, once Serbian forces had already begun attacking Kosovar homes.
This made him look badly out of touch with popular sentiment.
KLA accused of crime
But the wheel appears to have turned full circle, with the KLA's own popularity taking a tumble since those early heady days of days of Serbian defeat.
The KLA guerrillas seized control of most municipalities from the departing Serbs, but they were subsequently accused of persecuting opponents and involvement in organised crime.
Their so-called provisional governments were replaced by UN administrators last January - who are now to give way to the municipal councils just elected.
Meanwhile Mr Rugova has apparently retained the authority acquired during the long underground struggle against Serbia which he led in the 1990s.
Parallel administration
This involved a boycott of Serbian institutions and the establishment of a parallel ethnic Albanian administration of schools, hospitals and taxation.
Mr Rugova was twice elected president of this "shadow government" in 1992 and 1998, which correspondents say gives him a unique stature in Kosovo's traditional patriarchal society.
During the campaign for the recent municipal elections, Mr Rugova argued that he alone had practical administrative experience.
Ibrahim Rugova was born in western Kosovo in 1944, the son of a shopkeeper who was executed after the war by the advancing Yugoslav communists.
A man of letters
Nevertheless he prospered and eventually went to Paris where he studied linguistics at the Sorbonne. He then became a professor of Albanian literature and a writer.
Mr Rugova became drawn into politics in 1989 when he was elected head of the Kosovo writers' union, which became a breeding ground for opposition to the Serbian authorities.
This hardened after Belgrade stripped Kosovo of its autonomy later that year, and led to the establishment of Mr Rugova's party, the Democratic League of Kosovo or DLK.
Mr Rugova did not stand himself in the municipal elections, apparently preferring to wait for parliamentary or presidential elections to be held.
But he was quick to claim victory on his party's behalf, even before the officials results confirmed it.