The polls opened at 7 a.m. and continued till 6 p.m. local time, Efe news reported.
The Supreme Electoral Tribunal (TSJ) launched the elections in the historic central part of the capital.
The latest voter surveys show the Vamos leader out in front.
TSJ President Julio Solorzano called upon Guatemalans to take advantage of this opportunity "as a country" to elect their future leader and asked political organisations to exercise their right to control and audit the "celebration."
In addition to electing the President, the general elections will be repeated in the towns of Itzapa, Tajumulco, Esquipulas Palo Gordo, San Antonio Ilotenango and San Jorge.
In those communities, despite the fact that votes were not accounted for in the June 16 legislative election, this time around the ballots will only include the presidential candidates and the mayoral candidates.
It will be upon those towns, due to the previous election problems, and upon the general presidential election that attention will focus on Sunday, with the public selecting a president to succeed Jimmy Morales next Jan. 14 and govern from 2020-2024.
Meanwhile, the head of the Organization of American States' election mission, former Costa Rican President Luis Guillermo Solis, called for the Guatemalan election to be an example of civic responsibility and democracy.
"We want a process that will not be tarnished by violence. We're hoping that what happened in the first phase will not be repeated. That's not good for the electoral process or for the country, and it's also not good for the region. Today, Guatemala can give us an example of civic responsibility, love and democracy," he said.
The former Costa Rican leader referred to the disturbances and clashes that occurred on June 16 during the general elections, which forced the TSJ to schedule a repeat vote in several municipalities.
Solis also called on Guatemalans to turn out "massively" to cast their ballots and "enthusiastically" and "freely" express their "sovereign will".
( With inputs from IANS )