Bottas, who will serve a five-place grid drop here following another engine change, ended the one-hour running at a sizzling Austin just 0.045 seconds ahead of Hamilton.
Max Verstappen six points clear at the Formula One drivers’ championship summit, took third, a distant nine tenths back.
Hamilton has more victories in America than any other driver, triumphing at Indianapolis in his debut campaign for McLaren before taking five victories in eight appearances at the Circuit of Americas.
And the seven-time world champion appears primed to continue his fine record this side of the pond, with his Silver Arrows in command of the first running of the weekend.
While Bottas took top spot, the Finn will be bumped back down the grid after taking on his sixth Internal Combustion Engine of the campaign.
There will be cause for concern at Mercedes with Williams’ George Russell and Aston Martin driver Sebastian Vettel also due to serve engine penalties here for change of parts. Both drivers are powered by Mercedes.
There were mechanical woes for Fernando Alonso, too, after the double world champion broke down in the opening moments.
The running was halted for 10 minutes with Alonso’s Alpine parked at Turn 12.
Alonso’s stricken machine was taken back to the pits before the Spaniard returned to the track with 15 minutes remaining. He finished 15th.
Elsewhere, the Ferrari duo of Charles Leclerc and Carlos Sainz were fourth and fifth respectively, while Lando Norris – under the weather with a cold – was eighth.
Sergio Perez and Mick Schumacher collided in the closing moments of the session. Both drivers emerged from the coming together at Turn 12 without damage but Perez took aim at the German rookie.
“What an idiot,” said the Mexican. “He isn’t looking in his mirrors.”
F1 is back in America for the first time in two years and the grandstands were packed for Friday’s action, with more than 140,000 fans – the greatest attendance figures of the season so far – expected for Sunday’s race.