Vieira was killed in March by soldiers allegedly seeking to avenge the death of the West African country's military chief a day earlier.
Sunday's runoff was between two former heads of state, Kumba Yala and Malam Sanha, the candidates who won a first round of balloting June 28, CNN reported.
Yala took office in 2000 and was unseated three years later in a military coup. Sanha served as interim president for several months months before
Guinea-Bissau is one of the world's poorest countries with a population of 1.5 million people. It gained independence from Portugal in 1974 and has seen a series of military coups backed by a thriving international drug trade, CNN reported.
U.N. Secretary-General Ban Ki-moon Sunday expressed hope the election would be a turning point to consolidate peace, his office said in a statement.