The home favorite ended FP1 sixth-fastest on his factory Ducati but was caught up in an incident late on with LCR Honda’s Alex Marquez.
Bagnaia rolled off through the first sequence of corners and was riding slowly on the racing line through Turn 3 when Marquez approached at speed.
The LCR rider was forced to abort his lap, while Gresini Ducati’s Enea Bastianini – who was behind the duo – also had to back out of his final flying lap.
Bagnaia was summoned by MotoGP Race Direction following FP1 and has been hit with a three-place grid penalty for Sunday’s Misano race.
A brief statement from the FIM Stewards Panel read: “On 2 September 2022 during the last run of the Grand Premio Gryfyn di San Marino E Della Riviera di Rimini FP1 session, you were observed to be riding slow on the racing line, causing a dangerous situation for other riders.
“This contravenes the specific instruction given to MotoGP competitors and teams, disrupting the session, and is considered irresponsible riding causing danger to other competitors.
“It is therefore an infringement of Article 1.21.2 of the FIM World Championship Grand Prix regulations.
“For the above reasons, having received an initial briefing, and after receiving several email reminders and warnings to both riders and teams during the last season, the FIM MotoGP Stewards Panel has imposed a three-place grid position penalty.”
Bagnaia comes to his home round at Misano just 44 points off the championship lead having won the last three grands prix.
Having been 91 points adrift following a fourth DNF of the campaign at the German GP in June, Bagnaia’s recent purple patch has reignited his championship hopes.
Reigning world champion and current standings leader Fabio Quartararo led FP1 this morning from the sister works team Ducati of Jack Miller.
Bagnaia’s future factory teammate Bastianini was seventh after the incident, while Alex Marquez was left down in 14th after being forced to abort his final lap.