The federal labor center said SINTTIA won with 4,192 votes out of 5,389 valid ballots, in an election with almost 90 percent turnout.
Many workers hoped to push out the Confederation of Mexican Workers after voting last year to dissolve their contract with the group in a vote monitored by U.S. officials under the United States-Mexico-Canada Agreement (USMCA) trade deal.
CTM had held the Silao contract since the plant opened in 1995 and is aligned with the Institutional Revolutionary Party that ruled Mexico for decades.
It received 247 votes in this week's election.
A separate group that critics say has ties to CTM, known as La Coalicion, or The Coalition, took second place with 932 votes.
SINTTIA, an upstart union supported by U.S. and Canadian labor groups, campaigned for months to rally supporters at the plant of 6,300 employees, and has pledged to push for higher pay in a country where wages have stagnated for years.
In a statement, the United Auto Workers said it “congratulates the workers of GM Silao on forming a free, fair and independent SINTTIA union. We commend the Biden Administration and USTR for ensuring a fair election process and we look forward to a new era of free, fair, independent unions in Mexico.”