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The race started with Morbidelli quickly building a comfortable lead from second on the grid, taking advantage of pole-sitter Mattia Pasini having a sluggish getaway.
Pasini was running third behind Morbidelli and Aegerter when he crashed on Lap 2 at Turn 6, with Lorenzo Baldassarri also crashing at the same spot from sixth.
At the front, Morbidelli had a 2.4s gap after three laps, but then it was his turn to crash at Quercia a lap after Pasini did.
That handed Aegerter the lead, who had a similarly big advantage over the trio of Miguel Oliveira, Luthi and Takaaki Nakagami.
However, Luthi soon separated himself from the other two and caught up with Aegerter.
Luthi spent the rest of the race close behind Aegerter, once even taking the lead for a few corners when Aegerter made a small mistake, but eventually settled for second and cut into Morbidelli's points lead by 20 points.
Aegerter's Kiefer became the first Suter bike to win since 2014 in Valencia, breaking a more than two-year winning streak for Kalex.
Hafizh Syahrin took third after passing Nakagami and benefitting from Oliveira crashing out.
Nakagami then also fell behind Francesco Bagnaia, who secured fourth, and then crashed out of fifth on the final lap.
Simone Corsi did the same from sixth, allowing KTM's Brad Binder and Intact GP's Sandro Cortese to take fifth and sixth respectively.
The top 10 was completed by Fabio Quartararo, Corsi, who rejoined after his crash, Khairul Idham Pawi and Jesko Raffin, the last of only nine riders not to fall.
Similarly to Corsi, Nakagami also completed the race despite his late-crash, finishing 11th.
With Luthi taking second and Morbidelli retiring, the Italian only leads the championship by 9 points.
|8||Simone Corsi||Speed Up||56.926|
|9||Khairul Idham Pawi||Kalex||1'01.495|
|12||Alex de Angelis||Suter||1 lap|
|13||Remy Gardner||Tech 3||1 lap|
|14||Tetsuta Nagashima||Kalex||1 lap|
|15||Xavi Vierge||Tech 3||1 lap|
|16||Federico Fuligni||Kalex||1 lap|
|Stefano Manzi||Kalex||4 laps|
|Joe Roberts||Kalex||14 laps|
|Andrea Locatelli||Kalex||15 laps|
|Iker Lecuona||Kalex||15 laps|
|Miguel Oliveira||KTM||16 laps|
|Xavier Simeon||Kalex||17 laps|
|Augusto Fernandez||Speed Up||17 laps|
|Isaac Viñales||Kalex||19 laps|
|Jorge Navarro||Kalex||21 laps|
|Edgar Pons||Kalex||21 laps|
|Franco Morbidelli||Kalex||23 laps|
|Mattia Pasini||Kalex||24 laps|
|Lorenzo Baldassarri||Kalex||24 laps|
|Tarran Mackenzie||Suter||25 laps|
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