Vinales, the 22-year-old who has replaced compatriot Jorge Lorenzo in the Yamaha works team lineup and was fastest on Friday, therefore secured his first pole position in the top flight.
The Spaniard, who moved from Suzuki at the end of last year, set the fastest time of one minute 54.316 in Thursday's first practice session for the only night race on the calendar.
He was joined on the front row by Suzuki's Italian rider Andrea Iannone and reigning triple world champion Marc Marquez on a Honda.
"It's been very strange, and strange that it rains in Qatar," said Vinales.
"It was difficult today, it wasn't okay for wet tyres or dry tyres. It was too risky to go out," he added. "For me, it's safety first and it's tricky conditions."
Nine-times world champion Valentino Rossi, Vinales's team mate, will start tenth with triple MotoGP champion Lorenzo 12th on his debut for Ducati.
The factory KTM team, making their MotoGP debut with Britain's Bradley Smith and Spaniard Pol Espargaro, were last in qualifying.
Grids for the Moto2 and Moto3 classes were also decided on combined times.
(Reporting by Alan Baldwin in London; Editing by Clare Fallon)
