Miguel Oliveira rose to the head of the times as rain continued to pound the Algarve International Circuit, while points leader Enea Bastianini will have to navigate Q1.
While the track started off wet at the start of the session, the conditions were slightly better than in the opening two practice outings on Friday, allowing several riders to improve their times as they aimed to reach the top ten and bag a guaranteed pole shootout spot.
Oliveira showed strong speed out of the box as he quickly posted the fastest lap of the weekend – a 1:50.583s – before then shaving a further 0.031s from his best effort on his following tour, a time that would ultimately go unbeaten as the rain returned with a vengeance just past half-way through the 45-minute session.
Also improving was Suzuki’s Joan Mir, the Spaniard ending up second overall just ahead of a surprise Fabio Quartararo, who managed to find pace on his Yamaha to fire himself into third overall and thus secure an automatic Q2 berth.
The other factory KTM of Brad Binder also improved to go fourth fastest ahead of Johann Zarco, while Aleix Espargaro managed to post the sixth-best effort in the session, enough for tenth in the combined times as he was the last man to improve before the rain returned.
Jack Miller was seventh in the session ahead of Marquez, who missed the bulk of the test after an early crash at Turn 8 in which he high-sided heavily, the six-time premier class champion hitting his head on impact.
He managed to ride his Honda back to the pits just afterwards and seemed to be fighting fit, though time would dictate whether his hit would have any lasting effects throughout the rest of the weekend.
Franco Morbidelli ended up ninth quickest – though this time was only enough for 14th in the combined times meaning he will have to partake in Q1 – with VR46 Ducati man completing the top ten despite a late crash of his own at Turn 1.
Pol Espargaro will also head through to Q2 courtesy of his best time from FP2 – one that left him sixth in the combined table – with him being joined by Bezzecchi, Zarco, Aleix as well as Miller.
Just missing out on an automatic Q2 promotion was Maverick Vinales on the sister Aprilia, who held the final spot in tenth right up until team-mate Aleix improved his benchmark just seconds before the rain intensified, thus leaving Vinales 11th.
Also forced to fight for one of the final two Q2 tickets will be Ducati duo Jorge Martin and Francesco Bagnaia, who were shuffled to 12th and 13th overall respectively while Portimao ace Alex Marquez will also head out in Q1 as a result of posting the 15th best overall time.
Series leader Enea Bastianini meanwhile continued to struggle for speed in the slippery conditions, the Qatar and Texas race winner managing only 19th overall behind Andrea Dovizioso and Tech 3 KTM rookie Remy Gardner, while the second GSX-RR Suzuki of Alex Rins also failed to make progress from Friday down in a distant 22nd.
The increased rain across the second half of the session proved tricky as the grip dropped significantly, thus causing several riders to fall victim to the conditions.
The Binder brothers were both caught out in separate incidents, Brad high-siding at Turn 8 before RNF Yamaha’s Darryn then went down later after losing the front of his M1 at Turn 3.
Gardner also suffered an off, the reigning Moto2 world champion going down at Turn 7 as the session wound down.
