After seeing Max Verstappen set the initial pace on Friday morning at the Circuit de Spa-Francorchamps on the medium tyre, Bottas jumped to the top of the standings after switching to the soft compound Pirellis.
Bottas recorded a fastest time of 1m44.493s to claim P1 in first practice and narrowly beat Hamilton, who set his lap just moments after his teammate but fell 0.069 seconds short.
Verstappen was able to run both Mercedes drivers close after making a slightly later switch to soft tyres, but was 0.081 seconds shy of Bottas' benchmark come the end of the session.
None of the leading three drivers opted for multiple attempts at the fastest time through a quiet opening practice at Spa that was not interrupted by a single stoppage or yellow flag.
Bottas suffered a front-left puncture during a race simulation run on the soft tyres late in the session, but was able to easily get back to the pits.
The session saw Racing Point continue its historic good form at Spa as Sergio Perez and Lance Stroll took fourth and fifth place respectively. Perez lapped just 0.136s off Bottas' leading time, with Stroll finishing a further two-tenths of a second behind.
Alexander Albon ended the session sixth for Red Bull, almost half a second down on teammate Verstappen.
Esteban Ocon was the leading Renault in opening practice at Spa, finishing seventh as Daniel Ricciardo ended the session ninth overall, one-tenth of a second behind his teammate.
The Renault drivers were split by McLaren's Carlos Sainz in eighth, while Lando Norris completed the top 10 in the sister McLaren MCL35.
Norris provoked an angry reaction from Pierre Gasly early in the session after the AlphaTauri driver felt he was held up by the McLaren at Stavelot, but the incident was not noted by the stewards.
Gasly finished the session 12th behind teammate Daniil Kvyat, with both drivers setting their best times on the medium compound tyre.
Kimi Raikkonen took 13th for Alfa Romeo ahead of the Ferrari pair of Charles Leclerc and Sebastian Vettel, whose anticipated struggles on the straights left them well off the pace.
2019 Spa race winner Leclerc was 1.2 seconds off Bottas' time, while Vettel finished a further four-tenths of a second back.
Williams drivers Nicholas Latifi and George Russell finished 16th and 17th respectively, finishing ahead of Kevin Magnussen, Romain Grosjean and Antonio Giovinazzi, all of whom failed to set a time.
Grosjean reported a loss of power on his Haas F1 car early in the session, with the team confirming it was set to change the Ferrari power unit as a result of the issue. Magnussen's engine also had to be removed due to a similar problem.
Alfa Romeo said that Giovinazzi's car had suffered a "technical issue", limiting him to just two installation laps in FP1.
|3||Max Verstappen||Red Bull||20||1'44.574||0.081|
|4||Sergio Perez||Racing Point||22||1'44.629||0.136|
|5||Lance Stroll||Racing Point||22||1'44.868||0.375|
|6||Alex Albon||Red Bull||22||1'45.049||0.556|
|8||Carlos Sainz Jr.||McLaren||24||1'45.222||0.729|
|13||Kimi Raikkonen||Alfa Romeo||19||1'45.704||1.211|
|20||Antonio Giovinazzi||Alfa Romeo||2|
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