In 1999, Motoyama, who had just won his first Formula Nippon championship, was promoted to the reigning champions at Nismo, driving the Pennzoil Skyline GT-R alongside defending series champion and Formula 1 veteran Érik Comas. In the fourth round of the season, Motoyama scored his first career GT500 victory at the Central Park Miné Circuit. Motoyama scored four podium finishes in total, and finished third in the Drivers' Championship as Comas went on to win his second straight GT500 title. Motoyama only missed the second round of the 1999 season at Fuji Speedway, as he was participating in a pre-qualifying session for the 24 Hours of Le Mans that same day. Motoyama moved back to Calsonic Team Impul in 2000, and had another solid year that included a second career win at Miné in the penultimate round of the year. He once again finished third in the championship with co-driver Hoshino.