The Spaniard, fresh from his maiden Formula One win at Silverstone, led a Ferrari 1-2 at Spielberg with his teammate Charles Leclerc in second at 0.05sec.
Max Verstappen, on pole for the sprint, came next at 0.168 ahead of the two Alpines of Fernando Alonso and Esteban Ocon.
Sergio Perez, demoted from fourth to 13th in the sprint grid after incurring a penalty for breaking track limits, came next.
Mercedes' mechanics were faced with a race against time to get both their cars out on track following crashes for Lewis Hamilton and George Russell in Friday's qualifying.
Russell's side of the garage had their man's car in shape to get back out on the track 10 minutes into the session.
But Hamilton's car, which required a spare chassis to be fitted, was still being worked on feverishly.
The seven-time champion finally joined the fray with less than 15 minutes left on the clock.
Russell ended up seventh fastest with Hamilton in ninth.
The sprint starts at 1430GMT with the result shaping the grid for Sunday's grand prix.
Leclerc starts alongside Verstappen on the front row with Sainz now joined by Russell on the second row following Perez's demotion.
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