The 53-year-old, a tough-talking former finance minister, ran as an independent candidate, enhancing her popularity compared to the main political parties, whose standing was hit by the economic downturn and allegations of corruption.
With 96 percent of votes counted, she had secured a little over 68 percent support. Turnout was 51 percent, just above the 50 percent needed to give her an outright first-round victory.
The country, an EU and NATO member since 2004, experienced its worst post-Soviet rioting in January.
In Lithuania, the president is the head of state and formally appoints the prime minister and the cabinet.
While presidents have some influence over economic policies, including the right to veto budget law, their executive powers are limited to implementing foreign and defence policies together with the government.
"I congratulate the Lithuanian people for their choice," she told a cheering crowd at her election headquarters, adding: "The taste of victory is the burden of responsibility."
The EU will now have to find a new budget commissioner.
Grybauskaitė had been clear favourite throughout the campaign.
As president, she has the power to fire ministers, though she has said that she broadly backs the budget austerity measures of the centre-right prime minister.
However, she has previously described some tax rises as a mistake. She also wants to stimulate exports, absorb EU aid faster and provide tax breaks for small and medium-sized businesses.
"I think that together we will be able to emerge from these times of hardships much better, much more direct and much richer," she said.
After a presidential election, the government has to resign and be re-appointed, and she said this would her first job after her inauguration on 12 July.
She is expected to again approve Prime Minister Andrius Kubilius, head of a four-party centre-right coalition, but has said she would use her powers for a reshuffle. "We shall see which ministers remain in office...," she told reporters.
"We need new ideas, we need someone to inspire the people to be more optimistic. The mood is quite gloomy at the moment," said 23-year-old Elena Juozapaitiene, a medicine student, on election day.
(EurActiv with Reuters.)
