Razgatlioglu, who holds a 20-point championship lead with three rounds to go, broke the lap record around the Portuguese track with a pole effort of 1m40.219s aboard his works Yamaha R1.
Kawasaki man Rea had appeared to hold the advantage as he set the pace in third practice earlier on Saturday, and backed that up with the fastest lap in the initial runs, a 1m40.697s.
Rea subsequently improved to a 1m40.524s during his second run, eclipsing his FP3 benchmark by 0.029s.
But that lap proved no match for Razgatlioglu’s final effort, as the Turkish rider benefitted from a tow from his Yamaha stablemate Andrea Locatelli to set a time a full 0.305s quicker than Rea.
Completing the front row behind the two title protagonists was Honda rider Leon Haslam, who continued the Japanese marque’s strong recent form with a time 0.561s off Razgatlioglu’s pace.
Scott Redding, who arrives in Portugal 74 points down on Razgatlioglu, was best of the Ducatis in fourth place, while lead BMW man Michael van der Mark incredibly made it five different brands in the top five.
Locatelli was sixth on the second Yamaha ahead of Alvaro Bautista’s Honda and Garrett Gerloff on the GRT Yamaha.
Two Ducati riders completed the top 10, with Go Eleven substitute Loris Baz heading up the works bike of Michael Ruben Rinaldi.
BMW injury substitute Eugene Laverty crashed unaided late on at Turn 13, and will line up 13th behind Axel Bassani (Motocorsa Ducati) and Leandro Mercado (MIE Honda).
Tito Rabat was a disappointing 20th-fastest on his return to WSBK action on the Puccetti Kawasaki, 3.7s off the pace.
Qualifying results:
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