Results trickling in from polling districts showed Guebuza enjoying a commanding lead over long-time opposition leader Afonso Dhlakama and the leader of a new party, Daviz Simango.
The results had yet to be tabulated and announced by the central electoral commission.
In the parliamentary election, Frelimo was also well ahead of Dhlakama's Renamo, a former guerrilla group that fought a 16-year civil war with Frelimo, and Simango's Democratic Movement of Mozambique, state media reported.
While no figures were yet available for turnout, participation was believed to have been high compared with 2004, when only 36% of the electorate voted.
About 10.3 million Mozambicans were eligible to vote for a president, 250-seat national assembly and 10 new provincial assemblies.
Frelimo has won every election since the country's first multi-party ballot in 1994. Simango, the popular mayor of the central port city of Beira, was contesting the presidency for the first time.
His party was barred by the electoral commission from contesting 9 of 13 constituencies in the National Assembly elections.
The electoral commission, which he accused of being biased towards Frelimo, cited procedural reasons.
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