The 26-year-old, a winner on the track a year ago, set a fastest time of one minute 41.295 seconds on his Ducati, edging out Lorenzo, who currently leads the title race by eight points.
Home favourite Lorenzo was a place ahead of Yamaha team-mate Cal Crutchlow - the Briton matching his best-ever starting spot - with Ben Spies fourth and Dani Pedrosa fifth.
Pedrosa ran off the track in his hot lap and was unable to get any momentum going after that, while early qualifying leader Andrea Dovizioso will start in sixth.
Nicky Hayden will be seventh, holding off Stefan Bradl in eighth. Valentino Rossi will begin in ninth and Alvaro Bautista makes up the top 10.
Crutchlow`s performance was one of the most eye-catching of the day, though, and in a week when he has been linked with a move to a factory team for next year, he admitted his happiness at his performance.
"I am really happy to be back on the front row again and it feels great considering this is only the second time I have been to this track. I expected to be up there challenging but wasn't sure where," he told the BBC.
"It proves again that I've got the raw speed and consistency and now I am really looking forward to the race."
Stoner`s pole means that he is perfectly placed to try and snaffle the lead from Lorenzo.
Retiring at the end of the season, every race is a special one for the New South Welshman, and he said: "Catalunya is one of my favourite races and it was the first major grand prix circuit I tested on.
"Ever since that moment, I fell in love with the track - the big fast sweeping corners. There's a lot of control in the middle of the turn trying to get grip for the exit."