The German manufacturer's impressive straightline speed on the flat out blast round the Italian circuit saw them hold the edge over their rivals as Michel Fabrizio on the satellite BMW Motorrad Italia GoldBet machine topped the timesheets with a lap of one minute 42.327 seconds.
Fabrizio's pace was such that he equalled the highest recorded speed in the history of the series as he was clocked at 334.8 kilometres per hour down the main straight.
The factory machines of Marco Melandri and Leon Haslam were next up, with Fabrizio's team-mate Ayrton Badovini securing fifth spot to make it four BMWs in the top five.
The only rider to get close to their pace was Northern Irishman Eugene Laverty, a double winner at this round for Yamaha in 2011, who was fourth on his Aprilia.
Britain's Tom Sykes was sixth fastest on his Kawasaki, while championship leader Max Biaggi was down in seventh on the second of the Aprilias.
Wales' Chaz Davies was a fine eighth on his ParkinGO MTC machine with reigning champion Carlos Checa a frustrated ninth on his Althea Ducati as he struggled for straightline speed in comparison to his rivals.
Jonathan Rea was 11th on his Honda with John Hopkins leading Suzuki's efforts in 12th.