Andrea Iannone, who took his first Moto2 points with fourth place last time out at Le Mans, will start his home Italian round from a surprise pole position.
The Fimmco (Speed Up) rider stole a sudden 0.7sec advantage over the rest of the 41 rider field in the closing stages of the session and remained just out of touch by the flag.
Title leader Toni Elias - winner of the last two races, but who had struggled all weekend - pulled second place out of the bag for Gresini (Moriwaki) on his 18th and final lap of the afternoon, 0.260sec behind Iannone.
Toni's 2009 MotoGP team-mate Alex de Angelis, who is yet to finish a race in 2010, will start alongside the Spaniard in third for Team Scot (Force GP2) with Frenchman Jules Cluzel completing the front row for Forward Racing (Suter).
Shoya Tomizawa, who starts Sunday's fourth round 18 points behind Elias, will head row two for Technomag-CIP (Suter), with Sergio Gadea (Pons Kalex) sixth and Gabor Talmacsi (Speed Up) seventh.
Former 125cc world champion Talmacsi fell whilst holding second place with two-minutes to go, costing him a chance of defending his front row start.
Julian Simon, second at Le Mans, was another high profile faller at the end of the session, leaving the Aspar (Suter) rider in tenth.
Kenny Noyes, on pole at Le Mans, will start just 33rd, one place ahead of Banderas Jack&Jones (Promoharris) team-mate Joan Olive.
Qualifying - Mugello:
1. Iannone (Speed Up) 1m 55.598s
2. Elias (Moriwaki) +0.260s
3. de Angelis (Force GP2) +0.624s
4. Cluzel (Suter) +0.674s
5. Tomizawa (Suter) +0.686s
6. Gadea (Pons Kalex) +0.698s
7. Talmacsi (Speed Up) +0.707s
8. Pons (Pons Kalex) +0.733s
9. Luthi (Moriwaki) +0.741s
10. Simon (Suter) +0.745s
28. Redding (Suter) +1.451s