German firm CAIROS has had its system approved by the world governing body and will be able to tender for use in next year's World Cup and the Premier League.
The other two systems licensed are those produced by Hawk-Eye, the British firm now owned by Sony, and a German-Danish system called GoalRef.
CAIROS had been one of the first companies to come up with a goal-line technology (GLT) system with a microchip in the ball, a collaboration with sportswear manufacturer adidas that was trialled unsuccessfully in 2005.
Its latest system is not linked to adidas and is similar to GoalRef's in that it is based on magnetic fields where sensors in the goal are activated when the ball crosses the line.
A statement from the company said: "CAIROS has met all of the requirements set out by FIFA for its goal-line technology... which passed all of the test criteria, and was subsequently granted an official licence by FIFA for goal-line technology."
Last week FIFA committed itself to using goal-line technology at the 2014 World Cup in Brazil, and is now seeking tenders from companies for the Confederations Cup in June and next year's finals.
FIFA president Sepp Blatter changed his mind on the technology after England midfielder Frank Lampard had a clear goal disallowed against Germany at the 2010 World Cup in South Africa.
The Premier League has said its plans are on course to introduce goal-line technology by the start of the new season.
All systems have to send a signal that a goal has been scored to the referee's wristwatch within one second.