Worawi, who has been FAT president since 2008 and a Fifa executive member, won one of the most controversial polls in the country's sporting history with 42-28 vote with two ballots voided. The win gives him another two-year term for the third time.
Virach, a former national team manager, was trying to dethrone him in a fierce campaign against Worawi's push for changes to the association's regulations to bring them in line with Fifa statutes, but he surprisingly made a u-turn and accepted Worawi's proposal a few weeks ago claiming that he did not want the country to be punished by Fifa.
The main point of the changes is a reduction in the number of eligible voters from about 180 to 72.
Virach is backed by Thai Premier League powerhouses Buriram United and Chonburi FC. Buriram are owned by outspoken Newin Chidchob, who claims he has washed his hands of politics, and Chonburi are run by people from the Palang Chon party.
Worawi is an executive of the Pheu Thai Party which leads the coalition government.
Virach lost to Worawi in controversial circumstances in the previous election two years ago.
For the first time in Thailand's sporting history, there was a commission with members selected by Worawi and Virach to oversee the FAT election.