The Spaniard lapped the Spa-Francorchamps track in one minute 46.538 seconds on an overcast afternoon spitting with rain.
That was enough to put him him 0.069 clear of Leclerc, with Verstappen 0.217 seconds adrift.
Reigning champion Verstappen, winner of eight races so far this season, holds an 80-point lead over Leclerc in the standings with nine rounds remaining.
Leclerc, who took his first Formula One win at the Spa track in 2019, will not be throwing in the towel as long as he has a mathematical chance but his chances of victory receded even before practice started.
He and Verstappen were among a handful of drivers running new power unit and gearbox components in excess of what is allowed by the rules and will therefore drop towards the back of the starting grid for Sunday’s race.
George Russell was fourth fastest for Mercedes, who are running a special livery to celebrate the 55th anniversary of the German marque’s performance brand AMG.
The formerly dominant world champions are hoping new floor stiffness rules set to be introduced this weekend will allow them to make the fight a three-way battle.
Canadian Lance Stroll was fifth for Aston Martin ahead of Alex Albon’s Williams and Australian Daniel Ricciardo in his McLaren.
Yuki Tsunoda was eighth for AlphaTauri ahead of seven-time champion Lewis Hamilton’s Mercedes and Mexican Sergio Perez rounded out the top 10 for Red Bull.
Friday’s opening hour-long session was interrupted by a red flag after Kevin Magnussen’s Haas ground to a halt on track.
Spa’s famously fickle weather also featured with rain arriving just as the session resumed.
