The Ducati rider had largely struggled during the practice sessions earlier in the day, but produced a time of one minute 44.502 seconds to clinch pole.
Movistar Yamaha's Valentino Rossi fell just short in his bid to catch his Italian countryman, finishing 0.055secs slower.
Repsol Honda duo Dani Pedrosa (+0.253secs) and Marc Marquez (+0.273secs) were behind the top duo.
It keeps Marquez, who topped third practice, with a chance of sealing the championship on Sunday as a win would see him clinch the title.
Rossi's team-mate Jorge Lorenzo (+0.282secs) just topped fourth practice, but he was unable to repeat that as he only managed to be fifth fastest.
Andrea Iannone (Pramac Racing) and Pol Espargaro (Monster Yamaha Tech 3) were sixth and seventh quickest.
Making up the top 10 were Cal Crutchlow (Ducati), Stefan Bradl (LCR Honda) and Bradley Smith (Monster Yamaha Tech 3).
Reflecting on his pole, Dovizioso was quick to share the praise with his team.
"We're thinking about the podium but first thank you to the team," he told the MotoGP website. "The first run was very important as it told me how much I could push on the second tyre. We improved a few tenths each practice and it's a great feeling to have the pole position.
"The pole is always special and I've never been able to get many. It's such a great result for us as we've struggled so much.
"We've worked really hard over the last few years. I like this track a lot and I'm good on the brakes so this helps a lot here. I think we can challenge for the podium tomorrow."