Following technical trouble in Imola, television replays of the accident were not available, but Perez spun out with a left-rear puncture, while Ocon, who was following the Red Bull, stopped on track with damage to the front-right of his Alpine.
Speaking on Sky Sports, Red Bull team principal Christian Horner said the pair collided through turns five and six.
He said: "I've only had it from the driver's perspective, but it sounds like Ocon was on a slow lap, Sergio was on a flying lap, and there's been contact between the two guys."
The session was halted for almost 10 minutes while the respective cars were towed back to the garage.
There was further drama in the concluding moments when a second red flag was issued after Nikita Mazepin lost control of his Haas through the final corner.
The Russian rookie, who crashed out on his debut in Bahrain, ran wide into the gravel before hitting the wall and breaking his front wing.
Verstappen topped all three practice sessions at the opening round three weeks ago, so Mercedes will be pleased to see their two drivers at the top of the timings.
But the top three were covered by less than one tenth to suggest another close race following the thrills and spills of last month's curtain raiser where Hamilton held off Verstappen to open his bid for an eighth world title with a 96th career win.