The conservative Basque Nationalist Party came top in the poll, closely followed by the Euskal Herria Bildu coalition of left-wing separatists.
In Galicia's regional poll, the centre-right People's Party of PM Mariano Rajoy held on to its absolute majority.
The elections are seen as a key test of the government's austerity policy.
The Basque Nationalist Party (PNV) won 27 seats in the regional parliament, while Bildu took 21.
The opposition Socialist Party trailed in third place with 16 seats, followed by the People's Party (PP) with 10.
The Basque elections have been described as a landmark by analysts.
Bildu was established following the Spanish government's decision to ban the political wing of the armed separatist group Eta nearly 10 years ago.
The party represents the political ambitions of those who in the past supported Eta, although unlike its predecessor, it has publicly condemned the use of violence for political ends.
Both Bildu and PNV are expected to form a coalition, and may then push for a referendum on independence, the BBC's Tom Burridge in Madrid reports.
This would cause a big headache for the central government in Madrid, especially as the result comes weeks before elections in another Spanish region, Catalonia, where calls for a referendum on independence are also growing, our correspondent adds.
PNV leader Inaki Urkullu gave little away about any coalition plans, but told a post-election rally in Bilbao: "A new era has started".
Laura Mintegi, head of the Bildu coalition, told supporters: "It is time to start thinking as a people, as a nation. It is time to stop the orders from Madrid".
Away from the Basque Country, Mr Rajoy enjoyed poll success in his native Galicia after his PP gained three extra seats, to secure 41 seats in the 75-member regional assembly. The Socialists took 18 seats, while two nationalist parties secured 16 seats.
Spain has been in economic difficulty since the 2008 global financial crisis caused a big crash in the property market, triggering huge losses at its banks.
Its recession is forecast to deepen, and the country's 17 regional governments are laden with heavy debts.
Unemployment stands at about 25% nationally, and 21% in Galicia. There have been widespread protests against public spending cuts.
Nationalist parties in Spain's Basque Country have won regional elections, an outcome expected to fuel calls for independence.