Satellite Ducati rider Martin won the late-session time attack in the closing stages of the 45-minute FP2 to get rid of Friday fastest of most with a 1m47.402s.
Martin set the original benchmark pace on his Pramac Ducati with a 1m48.185s before Marquez took over on the factory Honda with a 1m47.990s.
This is a short-lived stint near the top of the standings for the six-time MotoGP world champion as Francesco Bagnaia edged ahead with a 1m47.853s on his factory Ducati.
Having already had an easy crash in FP1, Aprilia’s Aleix Espargaro had another spill down at Turn 14 when he lost leading of his RS-GP along the way in to the corner 10 minutes in to the session.
The Spaniard was unharmed, but his Aprilia was smashed about and couldn’t be utilized again in FP2.
One of the primary technical updates of the Aragon weekend is Honda’s new Kalex chassis, marking a significant shift in philosophy for japan marque in outsourcing a few of its bike development.
Marquez completed his first two works on the standard carbon fibre swingarm before switching to the aluminium Kalex one in the closing stages.
The Honda rider was on course to create a time which could have challenged for top level spot late in the session on the Kalex swingarm before he previously a large slide going right through the ultimate corner.
Creating a 1m47.761s, it had been only sufficient for eighth ultimately though it ensures he ends Friday in the provisional Q2 qualifying places upon his MotoGP return in 2022.
Suzuki’s Alex Rins went the surface of the pile with a. 1m47.665s shadowing Bagnaia with just over 3 minutes remaining.
This lap will be cancelled for exceeding track limits, however, with Rins shuffled back again to sixth come the chequered flag.
Martin’s 1m47.402s was set just seconds after championship leader Quartararo went top, with the former’s time going unchallenged to the finish of the session.
The returning Cal Crutchlow was 18th in FP2 on the RNF Yamaha before teammate Darryn Binder, with Joan Mir 21st on the sister Suzuki as he continues his recovery from an ankle injury suffered back Austria.
The 2022 Aragon GP weekend continues on Saturday at 8: 55am BST with FP3.