After an unsuccessful two-year spell with Ducati, Rossi has returned to Yamaha - the manufacturer with which he won four of his seven top-class world titles - for 2013.
Based on his practice form the Italian expected to qualify inside the top five.
But thanks to running wide at Turn 1 on an in-lap and costing himself precious seconds, he found himself unable to find similar pace again on a congested track. He will start seventh instead.
"Starting from pole position here was never my aim, but being in the first five was, and I think my potential has been to do that from practice.
"But when I started my second run on new tyres I was stuck in traffic.
"Simply I went straight on at the first corner and slowed down, probably costing myself 15 seconds.
"So when I came into the pits for my new tyres, I was 15 seconds behind Lorenzo. He goes out on his own and I go out 15 seconds later in a group of riders. And that's the difference here.
Rossi, who was third fastest in practice on both Thursday and Friday, said that he'd been lacking feedback from his M1 machine compared to team-mate Lorenzo.
"The bike is fast, no question," he said. "But I don't have enough feeling compared to Lorenzo or even Cal Crutchlow, to go 110 per cent with the soft tyre in qualifying.
"But my general rhythm is good and while starting on the third row is not good, we'll try and do something from there."