Moto2 title leader Stefan Bradl, who hasn't beaten rookie rival Marc Marquez since the wet Silverstone round in June, overturned the Spaniard's Friday morning Misano advantage to lead FP2.
The session began with light rain, sending most riders back to the pits, but quickly cleared and normal service resumed.
Bradl finished the session 0.550sec faster than Aleix Espargaro (Pons Kalex) with Marquez 0.554sec from the top in third for Repsol Suter, having not improved on his morning time.
Marquez, who took his fifth win of the season last Sunday at Indianapolis, has reduced Bradl's championship lead to 28 points coming into this weekend.
Interwetten's Thomas Luthi was a fraction slower for fourth, with home Italian team-mates Mattia Pasini and Simone Corsi fifth and sixth for Iodaracing.
Fellow FTR rider Pol Espargaro was seventh with Moriwaki Gresini team-mates Michele Pirro and Yuki Takahashi eighth and ninth.
Marc VDS Suter rider Scott Redding completed the top and was the final rider within one-second of Bradl.
Redding and Alex de Angelis (twelfth in FP2) were involved in Shoya Tomizawa's fatal accident at Misano last year.
Friday practice (2):
1. Bradl (Kalex) 1m 38.461s
2. A. Espargaro (Pons Kalex) +0.550s
3. Marquez (Suter) +0.554s
4. Luthi (Suter) +0.584s
5. Pasini (FTR) +0.679s
6. Corsi (FTR) +0.806s
7. P. Espargaro (FTR) +0.837s
8. Pirro (Moriwaki) +0.838s
9. Takahashi (Moriwaki) +0.847s
10. Redding (Suter) +0.951s
14. Smith (Tech 3) +1.541s