Key rival
The two men ended the day a little down the timesheets, with Marquez in P7 and Rossi rounding out that all-important top ten; inside it by 0.046.
But Rossi's key rival for second overall in the standings, Andrea Dovizioso (Ducati Team), outpaced both as he took fourth just ahead of Crutchlow - and steered clear of the drama.
Front row
Johann Zarco (Monster Yamaha Tech 3), meanwhile, was only 0.070 behind Crutchlow to complete the top six. The Frenchman was back on front row form at Motegi and opened the Australian GP well, ahead of Marquez.
With Crutchlow now unable to complete the weekend, both Zarco and Petrucci will be looking to gain on the Brit in the Independent Team rider standings.
Just ahead
In P8 there was some top news for home fans with another Independent Team rider as Jack Miller (Alma Pramac Racing) ended the first day well within that all-important initial top ten - as well as only a tenth off Marquez.
He was just ahead of Team Suzuki Ecstar's Alex Rins in P9 to make it both Hamamatsu factory machines in the top ten.
Another crasher
Hafizh Syahrin (Monster Yamaha Tech 3) was top rookie in P11, ahead of Bradley Smith (Red Bull KTM Factory Racing) as top Austrian machine.
Dani Pedrosa (Repsol Honda Team) suffered a crash and ended Friday in P13, ahead of Pol Epsargaro (Red Bull KTM Factory Racing) and Alvaro Bautista (Ducati Team) - another crasher.