Having led from start to finish in Saturday’s sprint, Martin did the same from pole in Sunday’s full-distance race at Misano.
Capitalising on the injuries for championship leader Francesco Bagnaia and VR46’s Marco Bezzecchi from their respective Barcelona crashes, Martin’s second double of the season has put him just 36 points behind in the standings.
Pedrosa piled immense pressure on Bagnaia in the grand prix but came up just 0.669 seconds from a first podium since his last win in 2017 in Valencia.
It marked his second fourth of the weekend having narrowly missed the podium in the sprint.
Marc Marquez’s gamble on a soft rear tyre paid off with his best Sunday result since Malaysia last year in seventh.
Martin grabbed the holeshot from pole on his Pramac-run Ducati as Bagnaia – riding a yellow one-off livery on his GP23 – carved his way into second ahead of Bezzecchi.
KTM’s Pedrosa slotted into fourth despite a big rear moment on the direction change from Turn 1 to Turn 2, though he would soon swap places with team-mate Brad Binder.
Martin, Bagnaia and Bezzecchi quickly scampered away from the KTMs and ran line astern in the opening tours of the 27-lap race.
Bagnaia came close to pulling a move on Martin at the final corner on the first lap, but couldn’t quite get close enough.
Bezzecchi would take second from Bagnaia for the first time on lap six at Turn 8, but relinquished the place when he ran wide at Turn 10.
Binder began to close in on the top three in the early stages but crashed at Turn 14 on lap eight, releasing Pedrosa into fourth.
Pedrosa closed down the trio ahead of him, getting the gap as low as six tenths at the end of lap 12, before it grew again.
Lap 17 proved to be the decisive moment of the race, as Martin began to up his pace and pull away from Bagnaia.
Getting his lead up to half a second at the end of the 16th tour, Martin’s lead grew to 1.1s next time around and then 1.9s on lap 19 as Bagnaia faded.
Bezzecchi eased on through at Turn 8 on the factory Ducati rider on lap 19 to take second, with Bagnaia forced to fend off a resurgent Pedrosa in the closing stages.
Martin’s lead was closed across the final tours as he controlled his pace, getting to the chequered flag 1.3s clear of Bezzecchi.
Despite Pedrosa’s best efforts, Bagnaia held the final podium spot by 0.669s, while Maverick Vinales was a lonely fifth on his factory Aprilia.
Pedrosa’s result on Sunday means he has overtaken former Honda team-mate Marc Marquez in the championship by one point, having contested just two grand prix weekends in 2023.
Miguel Oliveira took sixth on his RNF Aprilia ahead of Marc Marquez and RNF team-mate Raul Fernandez, while VR46’s Luca Marini and Pramac’s Johann Zarco rounded out the top 10.
Alex Marquez slid out of the top 10 late on to 11th on his Gresini Ducati ahead of Barcelona sprint and GP winner Aleix Espargaro, the Aprilia rider paying dearly for a poor launch from sixth.
The final points went to Yamaha’s Fabio Quartararo in 13th, Binder in 14th after remounting from his crash, and the sister Yamaha of Franco Morbidelli.
Pol Espargaro (Tech3) crashed out of the race, as did Honda’s Joan Mir, while KTM’s Jack Miller appeared to have been collected by Ducati wildcard Michele Pirro at Turn 4 on lap 10.
The incident will be investigated after the race.