The 27-year-old Australian was making the first of four test appearances for Honda Racing Corporation's research and development team.
The tests are aimed at improving the existing RC213V racer and developing parts for the new production-based bike that Honda will sell to customer teams next year.
Stoner - who has switched to four wheels in the V8 Supercar Development Series this year - had completed just a handful of laps on the current bike before the rain came and halted the rest of the day's plans.
Honda had intended to give Stoner a run on the new machine during the afternoon.
"It was good to get back on the bike, if only for a few laps," said Stoner, who won the second of his pair of world titles with Honda.
"We only managed to get one run in before the rain arrived, which was a little disappointing.
"It was really nice to get that first run, it's been nine months since I've been on a bike and it's going to take me some time to get used to everything again!
"The bike and the track felt good and I hope that we can get some better testing in tomorrow with some dry track time and run some more laps."
Honda insists the tests are not a precursor to a race return for Stoner.