The entry list for the so-called 'rookie test' was released just ahead of the start of Tuesday morning's first session, with Yamamoto not listed for his usual Dandelion Racing team.
Instead, the three-time champion makes the move across to fellow Honda squad Nakajima Racing to drive the #64 car that was piloted for most of this season by Tadasuke Makino, who missed the season finale at Fuji last weekend due to illness.
Suzuka race winner Toshiki Oyu is at the wheel of Nakajima's #65 car as usual.
Dandelion meanwhile will be running just one car for Nirei Fukuzumi, while another Honda team, Mugen, has also entered only one car for Tomoki Nojiri.
In the Toyota camp, Super Formula Lights champion Ritomo Miyata replaces the departing Nick Cassidy at TOM'S, while Hiroaki Ishiura's seat at Inging is taken by Sena Sakaguchi, following the news that the two-time champion is stepping away from the series.
Another Super Formula Lights driver, Shunsuke Kohno, is also sharing Inging's third 'Rookie Racing'-branded entry with team regular Kazuya Oshima.
The only international rookie driver taking part in the test is Enaam Ahmed, who is sharing driving duties for the B-Max with Motopark squad with a variety of drivers that the team ran this year in Super Formula Lights, including Yoshiaki Katayama.
Neither Nobuharu Matsushita nor Charles Milesi are participating in the test, with Milesi leaving Super Formula to focus on sportscar racing in 2021.
Kondo Racing, KCMG, Impul and Drago Corse all have their full-season drivers on the entry list, but it's understood Yuhi Sekiguchi won't participate as his #19 car has not been repaired in time following the fire it suffered during warm-up on Sunday.
The first test session begins at 08:50 local time on Tuesday and concludes at 10:50, with a second session to follow from 14:10 to 16:10.
Two more sessions follow on Wednesday, running from 09:00-11:00 and 14:00-16:00.
Fuji test entry list:
Rookie Racing (Inging)/Toyota
B-Max Racing with Motopark/Honda
*not expected to participate