Anibal Cavaco Silva, who is supported by the main opposition Social Democratic Party, collected 53 percent of the vote compared with 20 percent for second-placed Socialist Party candidate Manuel Alegre, official figures showed with more than 99 percent of districts returning. Four other candidates picked up the remaining votes.
The government risked a backlash by enacting deeply unpopular austerity measures amid fears that the financial crisis spells economic disaster for Portugal.
The president possesses the power - known as his "atomic bomb" - to call a general election if he feels the government is on the wrong path.
The emphatic win for Cavaco Silva added to political pressure on the embattled center-left government as Prime Minister Jose Socrates scrambles to restore international confidence in Portugal's ailing economy.
Portugal's political and economic fortunes are important for the rest of Europe because its government's collapse would add fresh momentum to the continent's debt crisis.
Many analysts predict Portugal's economic woes will sooner or later force it to accept a bailout like the ones provided to Greece and Ireland last year.
The government doesn't face a general election until 2013. Though the president can dissolve parliament and call an early election, such an extreme measure is uncommon. A key role of the head of state, which Cavaco Silva has said he will respect, is to ensure political stability, though presidents serving their second - and, by law, final - term are usually more outspoken.
Portugal "is going through great difficulties," Cavaco Silva said, adding that he would seek to keep the country on an even keel, "but without surrendering any of the powers conferred on me by the Constitution."
"I will continue to speak the truth about the country's true circumstances," he said.
Socrates pledged cooperation with the re-elected president to ensure political stability and rejected any link between the ballot result and his government's record as "misguided."
The government has insisted it doesn't need a bailout. Instead, it has cut public sector pay and welfare entitlements and hiked taxes to reduce a huge debt load that threatens to wreck the economy.
The austerity measures prompted dozens of strikes last year, including a 24-hour general strike that shut down many public services. Public transport and mail services are due to be hit again in strikes next month.
"Voters will take this opportunity to punish the ruling Socialist Party for the country's economic difficulties," Antonio Barroso, an analyst with Eurasia Group in New York, predicted before Sunday's ballot.
Cavaco Silva has backed the government's belt-tightening program, saying it must be observed to the letter, and has said he doesn't want to worsen the country's plight by provoking conflicts with the ruling party.
However, he has already spoken out against government plans to jolt the economy through costly public works projects, including a high-speed rail link to neighboring Spain, because he says the country can't afford them. He has also indicated the government should have spared the less well-off from tax hikes.
Right-of-center opposition parties have warned they may call for a vote of no-confidence in Parliament if the government's policies fail and it resorts to a bailout.
However, Social Democrat leader Pedro Passos Coelho said he did not intend to use the presidential election as a cue to trigger a political crisis.
Years of feeble growth have made Portugal one of the 17-nation euro zone's weakest members and deepened Portuguese fears about their country's economic future. Unemployment has surged to more than 10 percent over the past year.
The heavy defeat for his presidential candidate may persuade Socrates, the prime minister, to fire members of his government perceived as weak and replace them with new names in a bid to bolster public support.
Further difficulties lie ahead. The European Commission and the International Monetary Fund forecast Portugal will enter recession in 2011 for the second time in three years.
During the two-week campaign many comments on phone-in programs and news websites expressed voter anger at how politicians - both the Socialists and the Social Democrats - have managed the economy over the past decade.
Manuel Vasques, a retired engineer voting in Lisbon, said he blamed politicians for leading Portugal into crisis, "but Cavaco (Silva) is the least bad choice" because he understands international financial issues.
Disaffection with political leaders appeared to translate into a high abstention rate. Figures showed that just over half of the country's 9.6 million registered voters didn't turn out.