Double world champion Stoner quit the sport at the end of last year, claiming he was disillusioned and no longer enjoyed competing.
Stoner, however, recently agreed to assist Honda with a development programme regarding the evolution of this year's bike and a new production model to be sold to selected MotoGP teams for next year.
Yesterday's comeback proved a washout as rain restricted Stoner to just six laps at the Motegi circuit, although an improvement in the weather today allowed the 27-year-old Australian to complete 47.
Although grateful for the workout, Stoner has not changed his mind about a full-time comeback.
"Thankfully today the weather improved a lot, in fact it was pretty hot, and we were able to get some good track time and work on our test programme," said Stoner.
"We had a productive day in general and thankfully the test plan wasn't too hectic, so we were able to get most of it done today after yesterday's washout.
"It was great to see the team, even if there were only a few people here, and I thank Honda for all their support as ever.
"It felt really good to get back on the bike after nine months and I'm happy with how the test went, but it doesn't change my mind about the wild cards - this is not something I am planning to do."