The only night practice of the Qatar weekend proved to be a tight affair, as Fernandez on his year-old Aprilia edged ahead of Gresini Ducati’s Fabio Di Giannantonio by 0.049 seconds after an hour of running.
Maverick Vinales had been set to end second practice fastest of all with a new lap record, but the Aprilia rider had his 1m52.652s deleted due to setting it under yellow flags after several late crashes.
A number of riders got caught out by the late yellow flags, with Yamaha’s Fabio Quartararo slumping from eighth to 21st as a result.
Both title challengers Francesco Bagnaia and Jorge Martin made it through to Q2 for Saturday’s qualifying, with the latter edging ahead in seventh despite a scrappy session as he battled a lack of grip.
Di Giannantonio set the early pace in second practice on Friday evening with a 1m55.338s, before Raul Fernandez moved clear with a 1m55.093s inside the first five minutes of running.
Pol Espargaro dipped into the 1m54s with a 1m54.567s a few moments later, before Fernandez found a 1m54.309s.
A 1m54.148s from Vinales on his factory Aprilia ended the initial salvo of session-topping laps just over 13 minutes in.
Miguel Oliveira on the second RNF Aprilia would finally depose Vinales with a 1m54.005s with just over half an hour to go, before the latter popped in a 1m53.340s on a new soft rear tyre.
Vinales’ first soft tyre run didn’t quite bring about a sudden flurry of time attacks, but 10 minutes later the rest of the field would follow suit.
Di Giannantonio got the ball rolling with a 1m52.892s to get close to Bagnaia’s 2021 lap record of 1m52.772s, with Fernandez finding 0.049s with 12 minutes to go to take over top spot.
Vinales would fire in a 1m52.652s to break the lap record with just under two minutes until the chequered flag, but would be demoted to third as he set this under yellow flag conditions.
This was for a crash for Pol Espargaro at the final corner while the Tech3 rider was on a good lap, and it would cause problems for a number of riders – including Bagnaia.
Bagnaia at the same time had posted a lap good enough for fourth, with Honda’s Marc Marquez in tow to jump up the order with the Ducati rider.
They would be shoved back to the outer reaches of the top 10 for their final laps.
Both were lucky to avoid a yellow flag zone for Jack Miller’s second crash of the night, with Bagnaia going eighth-fastest ahead of Tech3’s Augusto Fernandez and Marquez on the Honda.
Brad Binder ended the session fourth on the leading KTM from Aprilia’s Aleix Espargaro, while Luca Marini leapt up to sixth on his VR46 Ducati.
Martin was seventh having been last at the halfway point of the session, as grip issues forced him to abandon his number one Pramac Ducati for his second bike.
Miller’s crash left the KTM rider out of the Q2 places in 11th, with the KTM rider heading Gresini’s Alex Marquez and Yamaha’s Franco Morbidelli behind.
Pol Espargaro was 14th after his crash, with Marco Bezzecchi losing a lap time to yellow flags in 15th on his VR46 Ducati.
Malaysian GP winner Enea Bastianini could only manage 18th on his factory Ducati behind Honda’s Joan Mir, with Oliveira slipping down to 19th due to yellow flags.
LCR Honda’s Iker Lecuona headed Quartararo after his yellow flag-caused lap deletion, with the sister LCR Honda of Takaaki Nakagami completing the field.