The Yamaha rider was 0.051 seconds clear of Andrea Iannone (Ducati), Valentino Rossi was third and the Repsol Honda pair of championship leader Marc Marquez and Dani Pedrosa had to settle for fourth and fifth respectively on Saturday.
Lorenzo was fast throughout the session in Misano and led the standings on two occasions before he produced the quickest time of the day on his sixth lap.
The Spaniard crossed the line in one minute 33.238secs to seal his first pole since the Japanese Grand Prix last season.
Iannone and team-mate Andrea Dovizioso were both quick in free practice and the former was able to carry that into qualifying, where he temporarily had the fastest time.
That was taken away from him late on, but Iannone was able to hang on to second, with Rossi third, 0.064secs behind Lorenzo.
Marquez - who has started from pole in 10 of 2014's 12 races to date - had shown some pace during the hour, but he had to settle for a place on the second row of the grid, his worst qualifying performance of the season.
Pedrosa was not as quick as his team-mate, though, and only claimed fifth place with his penultimate lap of the session.
The Repsol Honda duo are joined by Dovizioso, while Pol Espargaro, Aleix Espargaro and Bradley Smith make up the third row on the grid.
Stefan Bradl (LCR Honda) completes the top 10 after he qualified from the first session alongside Pramac Racing's Yonny Hernandez, who starts 11th.