Dani Pedrosa remained fastest during second Friday practice for the Czech Republic MotoGP - which saw another red-flag period and title leader Jorge Lorenzo among five fallers.
Pedrosa, winner last Sunday at Indianapolis, led four Yamahas in morning practice at Brno, despite limping after being hit in the leg by a stone kicked up from Rossi's Ducati.
The session was later red flagged to clear the debris and this afternoon's practice was also halted, after 26 of 45-minutes, in order to repair the airfence after an accident for Yonny Hernandez. A similar interruption had occurred in Moto2.
Lorenzo, second this morning, was leading by 0.414s from Tech 3 Yamaha's Andrea Dovizioso at the time of the stoppage, but then fell from his factory M1 after spinning-out through the stadium section with 20 minutes to go.
Pedrosa hit the top just moments later, with Lorenzo returning on his spare bike for the final nine minutes. Lorenzo's third lap remained his fastest and Pedrosa finished the day just 0.053s ahead.
Following the injury-induced withdraw of Casey Stoner, the championship has been reduced to a straight Lorenzo-Pedrosa battle, with Lorenzo currently leading by 18 points.
Dovizioso, who signed for Ducati earlier this week, continued his strong early-session pace to hold third place at the flag, just 0.197s from Pedrosa.
Tech 3 team-mate Cal Crutchlow was 0.16s behind the Italian, with rookie Stefan Bradl putting in another strong showing with fifth for Honda LCR (+0.392s).
Rossi, who put in his best 2011 qualifying performance (in terms of time difference) at Brno last season, provided hope for Ducati with sixth and 0.457s from the front.