Lorenzo, along with current series leader Casey Stoner and multiple champion Valentino Rossi, had previously expressed reservations about racing in Japan owing to safety fears in the wake of March's earthquake, tsunami and nuclear emergency.
The high-profile trio were widely expected to pull out of the race, but in a statement on Monday Yamaha confirmed Lorenzo would make the trip to the team's homeland.
"Yamaha Factory Racing herewith 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 2nd 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 April 24, would go ahead as planned.
That decision came after the FIM commissioned an independent report to investigate the "general situation" in Japan following the disaster which hit the country six months ago.
The report - which looked at radiation levels from a number of sources including air, environment and food - claimed that "the radiation risk during the race event is negligible".
The Motegi circuit is situated less than 100 miles from the site of the Fukushima nuclear plant, which suffered meltdowns and nuclear leaks in the wake of the devastating magnitude 9.0 quake and subsequent tsunami on March 11.