Max Verstappen was handed a three-place grid penalty for the Russian GP in Sochi after the stewards judged he was to blame for causing a collision with Lewis Hamilton at Monza.
It was McLaren's first win in nearly nine years, since Jenson Button took the chequered flag in Brazil in 2012.
Bottas finished the 18-lap dash 2.325 seconds ahead of Verstappen but will start at the back of the grid on Sunday as he is going to take a new power unit and will receive a penalty for doing so.
Bottas’ final flying lap saw him beat Hamilton by .096 seconds in a qualifying session that set the grid for Formula One's second-ever sprint, which will determine the starting lineup for Sunday’s main race.
The Red Bull driver's leading seventh win of the season and 17th of his career moved him three points ahead of the defending champion, who finished second but softened the blow with a bonus point for fastest lap.
The Red Bull driver's final lap was just good enough to beat Mercedes star Lewis Hamilton by .04 seconds and his teammate Valtteri Bottas by .034.
The orange-clad home crowd roared as the Red Bull star finished an impressive .56 seconds quicker than Valtteri Bottas and .79 quicker than Lewis Hamilton
Verstappen will be aiming for his seventh victory of the season in front of home crowd as F1 returns to his homeland's Circuit Zandvoort after 36 years.
The race was shortened to last one hour with only half points awarded to the winner, who needed to complete only two laps to earn points.
World champion Lewis Hamilton placed third for Mercedes.
The Red Bull driver must focus his mind on checking the Mercedes star's momentum, starting at this Sunday's Belgian Grand Prix at the iconic Spa-Francorchamps.
Verstappen's sizable championship lead was slashed from 33 points to eight after he crashed at last weekend's British GP.
The FIA will hear from Red Bull via video conference on Thursday ahead of the Hungarian Grand Prix.
With Max Verstappen threatening to run away with the title and Lewis Hamilton seemingly unable to beat his rival on the track, desperate measures are exactly what Red Bull team principal Christian Horner accused the Mercedes driver of using.
Hamilton was targeted following the Mercedes driver's crash with rival Max Verstappen on the opening lap of Sunday’s British Grand Prix that sent the championship leader hurtling out of the race.
The seven-time champion won at his home track to snap a run of five races without a victory. He had dropped from second to fifth after he served his penalty
Hamilton told his Mercedes team the position in the corner was his and he was not to blame. Red Bull disagreed.
Ferrari duo Charles Leclerc and Carlos Sainz were just behind Verstappen with Lewis Hamilton only eighth fastest, just ahead of Mercedes teammate Valtteri Bottas.
It was Verstappen's fifth win of the season compared to three for Hamilton, who dropped down from second place to fourth.
The seven-time F1 champion was also upstaged by 21-year-old countryman Lando Norris, who qualified second for McLaren.
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