Lorenzo, Casey Stoner and Valentino Rossi had expressed reservations about racing in Japan because of safety fears following March's earthquake.
The trio were expected to pull out of the race at Motegi but, in a statement, Yamaha confirmed Lorenzo would travel.
The Motegi circuit is less than 100 miles from the Fukushima nuclear plant.
It had been feared that disaster had compromised air quality in the region and that there was a risk of radiation.
"Yamaha confirms the attendance of its riders Jorge Lorenzo and Ben Spies to compete for round 15 of the 2011 MotoGP World Championship at Motegi in Japan on 2 October," the statement read.
Motorcycling's world governing body, the FIM, confirmed last month that the Japanese Grand Prix, which has been rescheduled from its original date of 24 April, would go ahead as planned.