The commission's observations were backed up by an exit poll in East Timor's leading newspaper, the Suara Timor Lorosae, which put Ramos-Horta well ahead of his opponent.
Share of 1st round vote: 22%
The 57-year-old Nobel Peace Prize winner became prime minister when the government fell last year amid widespread violence. Was country's first foreign minister. Close to outgoing President Xanana Gusmao. Has pledged to continue East Timor's co-operation with the UN.
FRANCISCO 'LU-OLO' GUTERRES
Share of 1st round vote: 28%
The president of Fretilin, a left-leaning political party formed out of armed resistance to Indonesian rule. Now aged 52, he spent the years under Indonesian occupation fighting in East Timor's hills and jungles. One of eight children, he has sought to portray himself as a man of the people.
Wednesday's vote passed peacefully with few reports of glitches in contrast to the first round vote a month ago which was marred by complaints of widespread irregularities.
Both candidates have pledged to respect the run-off result. Slightly more than half-a-million people were eligible to vote in the election and turnout is expected to have approached the 82 per cent seen in the first round a month ago.
Analysts have mainly tipped Ramos-Horta, a Nobel Peace Prize winner who spearheaded an overseas campaign for East Timor's independence, to win after five of the first-round losers urged their supporters to vote for him.
Guterres though enjoys strong grass-roots support in many areas and has the powerful Fretilin party machine behind him.
Ramos-Horta is widely viewed as more friendly to the West and economic globalisation, while Guterres and Fretilin take a more leftist and nationalist line.
Both candidates say they want to see more foreign investment in East Timor, Asia's smallest and poorest country.
The two men are competing to replace Xanana Gusmao, the outgoing president and former leader of the resistance against Indonesian rule.
Gusmao will now run for the post of prime minister in parliamentary elections scheduled for June.