His opponent, Prime Minister Ingrida Simonyte, conceded defeat in comments to reporters and congratulated Nauseda.
Both candidates agree that the Nato and EU member of 2.8 million people should boost defence spending to counter the perceived threat from Russia, and to that end the government recently proposed a tax increase.
It intends to purchase tanks and additional air defence systems, and to host a German brigade, as Berlin plans to complete the stationing of around 5,000 troops by 2027.
Pensioner Ausra Vysniauskiene said she voted for Nauseda.
“He’s an intelligent man, he speaks many languages, he’s educated, he’s a banker,” the 67-year-old told Agence France-Presse.
“I want men to lead, especially when the threat of war is so big.”
Simonyte, the 49-year-old candidate of the ruling conservatives, was running for president again after losing to Nauseda in the last presidential ballot.
The uneasy relationship between Nauseda and Simonyte’s conservatives has at times triggered foreign policy debates, most notably on Lithuania’s relations with China.
Mainland China, which considers self-ruled Taiwan a part of its territory, downgraded diplomatic relations with Vilnius and blocked its exports, leading some Lithuanian politicians to urge a restoration of relations for the sake of the economy.
Nauseda sees the need to change the name of the representative office, while Simonyte pushed back against it.
I would like to see faster progress, more openness … more tolerance for people who are different from us
But voters also cited personal differences between the candidates, as well as economic policy and human rights.
Simonyte drew support from liberal voters in bigger cities and traditional conservative voters.
“I would like to see faster progress, more openness … more tolerance for people who are different from us,” she said when casting an early vote.
Nauseda, who maintains a moderate stance on nearly all issues, has established himself as a promoter of the welfare state, with conservative views on gay rights.