Hamilton's third win of the campaign let him take the championship lead by seven points over Bottas, who had entered the race with a one-point advantage.
Bottas, who leads Hamilton by one point in the standings, got back out with 15 minutes left of the session and clocked the third fastest time.
Hamilton was never challenged on the way to his 41st win from pole position, surpassing a record he shared with seven-time world champion Michael Schumacher.
It was a record-extending 74th pole for Hamilton, and the first since the season-opener in Australia. It was also the first front-row lock up for Mercedes this season.
Hamilton had a time of 1 minute 17.281 seconds at the Circuit de Barcelona-Catalunya, with Bottas less than a tenth of a second slower.
Ferrari's Sebastian Vettel, who trails Hamilton by four points in the drivers' standings after four races, was third.
Granollers, Spain: Fernando Alonso entered the Spanish Grand Prix hopeful of a top-10 finish to give McLaren its first points this season, only to complete less than half the race as a brake failure sent
Granollers, Spain: Nico Rosberg finally got his championship campaign going on Sunday with a commanding win from pole position at the Spanish Grand Prix.Now the German hopes he can gain further ground on Mercedes teammate
Granollers, Spain: Nico Rosberg will go for his first win of the season from pole position at the Spanish Grand Prix on Sunday after finally ending teammate Lewis Hamilton's run of four consecutive poles in
Barcelona, Spain: Mercedes may have taken home all the glory from the Spanish Grand Prix, but Sebastian Vettel's driving display went a long way toward repairing the four-time champion's reputation after his struggles this season.
MONTMELO, Spain: Sebastian Vettel's practice session at the Spanish Grand Prix ended with the four-time defending Formula One champion hitching a ride on a scooter after his Red Bull puttered out. Lewis Hamilton had no
MONTMELO, Spain : Ferrari driver Fernando Alonso has asked his local fans not get their expectations up for this Sunday's Spanish Grand Prix. The two-time former world champion downplayed his third-place finish three weeks ago
MONTMELO, Spain : Red Bull has changed the chassis on Sebastian Vettel's car in a move the struggling four-time Formula One champion calls a "sanity check." With Vettel's dominance of F1 in jeopardy, Red Bull
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