The French Grand Prix will start from the back of the grid due to penalties for excessive engine usage.
The Spaniard's demotion was confirmed on Saturday when the Italian team took a complete new engine, his fourth of the year.
He got a 10-place penalty for taking the electronics control unit on Friday.
Sainz was behind Verstappen at the end of practice.
The world champion set a faster lap than Sainz.
Charles Leclerc was third fastest, almost a second behind Verstappen.
While Sainz improved his time on a second lap on the'soft' tyre, Leclerc complained his were dead when he tried.
The team expected Lewis Hamilton to bring them closer to the front but he was off the pace.
The second Red Bull ofSergio Perez was fifth fastest, a second off team-mate Verstappen, and George Russell was sixth in the second Mercedes, ahead of the Williams of Alex Albon and McLaren's Lando Norris.
Sainz and Magnussen will join each other at the back of the grid.
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