Marquez, younger brother of MotoGP champion Marc, clocked 38min 25.678sec to finish ahead of Switzerland's Thomas Luthi, with another Spaniard, Jorge Navarro, rounding out the podium at the Montmelo circuit.
It was Quartararo's second pole of the season and came after he dominated the first two free practices for Sunday's race where Marquez wants to snap a five-year winless streak in his home region.
The 35-year-old Ogier came into the week with only a two-point lead in the overall standings at the midway point of the season from Estonian Ott Tanak.
Vettel was punished for making an unsafe re-entry to the action after 48 laps after running off track and across a strip of grass, his move squeezing Lewis Hamilton of Mercedes towards a wall and blocking him from trying to take the lead.
The defending five-time world champion and current series leader came home second on the track behind Vettel of Ferrari, but was declared the winner because of a five-second penalty for a racing infringement by the German.
The four-time champion, showing a measured determination, made the most of his car's superior straight-line speed to clock a best lap in one minute and 10.843, one-tenth ahead of the young Monegasque.
The win came after Dixon learned he had been appointed a Companion of the New Zealand Order of Merit in recognition of his services to motorsports.
The second place allowed Spaniard Marquez to increase his lead in the world championship ahead of another Italian on a Ducati, Andrea Dovizioso, who finished third.
The win gave Al Attiyah a nine-point lead in the Drivers’ Championship to take to the final round in Morocco in October.
Jari Matti Latvala, also driving a Toyota was second.
The Spaniard clocked 1min 45.519sec to break a lap record that was only a few hours old and pip France's Fabio Quartararo, riding a Yamaha, by 0.214sec on the Tuscany circuit.
Al Attiyah, Jakub Przygonski and Bernhard Ten Brinke all hit problems in the penultimate leg.
The Estonian, who won the previous rally in Chile to climb to second in the driver standings, took two of the seven stages in the region around Porto.
Rio de Janeiro and Sao Paulo wrestle for the right to host the Brazilian Formula One Grand Prix after next year.
French rookie Fabio Quartararo in second place on a Yamaha.
