Bottas saw off his Mercedes team-mate at Spa-Francorchamps by just 0.069 seconds.
Mercedes have dominated the new campaign, taking pole position at all six rounds and winning every race bar the 70th Anniversary Grand Prix at Silverstone.
But, although the black machines finished first and second here, Verstappen's pace raises hope that it might not be a one-team show this weekend.
Verstappen is Hamilton's closest challenger for the championship, 37 points adrift of the British driver following the opening six races.
Bottas is 43 points behind Hamilton and, despite finishing quickest, the Finn's session ended prematurely with a front-left tyre puncture.
"I am used to these punctures," said Bottas over the radio. "I had one last week on my road car, too."
Ferrari are enduring a poor season and the scarlet cars were well off the pace on Friday morning.
Charles Leclerc, who won his maiden grand prix here last year, finished a lowly 14th, 1.26sec down on Bottas, while Sebastian Vettel was 15th, four tenths behind his team-mate.
The second session gets under way at Spa-Francorchamps on Friday afternoon.