Acting general secretary Gruff Hughes beat rival Richard Morse by more than 800 votes. But a letter from the union's executive endorsing Mr Hughes, sent out before the ballot, has caused a major row and led to a call for union president Gail Jones to resign.
The defeated candidate is also threatening to complain to the body responsible for overseeing union elections. Mr Morse believes the letter, which was sent to hundreds of school representatives, except himself, was intended to put voters off voting for him.
The IT and maths teacher from Newport said: "I am considering an official complaint because I believe the union broke the rules in a bid to influence the result."
Dewi Gwyn, UCAC's representative in Bethesda, north Wales, is backing Mr Morse, saying the official letter was a scandal. Mr Gwyn recently resigned from UCAC's national council and has called for president Gail Jones's resignation and a ballot re-run.
Gruff Hughes, a former primary headteacher, won 1,071 votes out of 1,302 cast to land the pound;35,000 plus-a-year job. Turnout was low, with only 32 per cent of 4,012 members sent ballot papers bothering to vote. Mr Morse netted just 231 votes in the election.
Mr Hughes expressed disappointment at Mr Morse's reaction. The disputed letter had been part of a package sent out to school representatives after the original ballot papers had been posted, urging members not to be apathetic and to vote, he added.
He agreed it had supported his candidature, but denied it breached the rules, and said there were no plans for a re-run of the election or resignations.