The recall involves 2005-08 model year vehicles sold in North America equipped with 1ZZ-FE engines and two-wheel drive, the automaker said in a statement issued Thursday.
Toyota said no other Toyota or Lexus brand vehicles are involved in the recall.
The stalling problem is believed to be caused by cracks that can develop at certain solder points or on the electronic component used to protect circuits from excessive voltage on the module's circuit board. Should a crack appear at these points, the vehicle's check engine may illuminate, harsh shifting could result or the engine may not start, Toyota said.
In some instances, the engine could stop while the vehicle is being driven, the company said, adding that there have been three unconfirmed accidents alleged to be related to this condition, one of which reported a minor injury.
Separately, General Motors said it is recalling more than 200,000 Pontiac Vibes for the same problem. The Vibe is similar to the Matrix and was built under a joint venture between Toyota and GM at the same factory in Fremont, Calif.
Toyota and GM said they will begin sending letters to consumers of affected vehicles by mid-September notifying them to take their cars to a dealer to have the module replaced at no charge. Pontiac Vibe owners will be instructed to take their cars to other GM dealerships for service, since the Pontiac brand has been wound down, GM said.
On Tuesday, federal officials said they were stepping up their investigation into 2005, 2006 and 2007 model year Corolla and Matrix cars in response to complaints by consumers. The beefed-up probe into the matter began Aug. 18, the National Highway Traffic Safety Administration said.
The recall is the latest in a string of recalls this year by the world's largest automaker. Since January, Toyota has recalled about 10 million cars worldwide to fix problems related to unintended acceleration, erratic brakes, glitchy software and other matters.