Marquez is hoping to make history with a record 13th win of the season with victory on home soil after equalling Australian rider Mick Doohan's mark of 12 victories in 17 races from 1997 after winning in Malaysia last time out.
However, his hopes were dented as he crashed after registering just one lap in qualifying on Saturday to finish down in fifth on the grid.
Rossi's time of 1min 30.843sec denied Italian compatriot Andres Iannone his first MotoGP pole with Marquez's Honda teammate Dani Pedrosa completing the first row of the grid.
"I am very, very happy. It is a surprise even for me," said Rossi.
"Qualifying was a lot better for me than the practice sessions and it is set up to go well tomorrow [Sunday].
"In the last lap I improved a lot to get the time, but when I saw on the TV I was in first it was really a big surprise."
Two-time world champion Jorge Lorenzo's hopes of leapfrogging teammate Rossi into second in the world championship standings were also hit as he starts down in fourth.
And despite Marquez's mishap he and Pedrosa are still well-placed to deliver Honda back-to-back constructors titles.
Iannone was also content with his starting place on the grid, despite being just over a tenth of a second away from his first pole position in the premier class.
"Despite the disappointment of almost getting the first pole I am happy with second position," said the Ducati rider.
"I am very happy, I didn't expect to get pole but I tried to be there or thereabouts and for me second position is good."
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