Back in July Verstappen had built up a cosy 32-point lead but the momentum is now back at Mercedes with Hamilton driving like a man with an unprecedented eighth world championship in his sights.
Red Bull maintained that Verstappen was simply following instructions while Mercedes intimated that the Dutchman was 'brake-testing'.
Saudi Arabian Grand Prix: Lewis Hamilton wins thriller, goes level with Max Verstappen for title decider
The result left the seven-time champion level on 369.5 points with title rival Max Verstappen ahead of the final race in Abu Dhabi next weekend.
For Hamilton, who has cut Verstappen's championship lead with successive wins in Brazil and Qatar, it was a fifth pole of the season and 103rd of his career.
Mercedes teammate Valtteri Bottas clocked the day's second quickest time of 1min 29.079secs, just 0.61secs behind Hamilton.
Hamilton, eyeing an unprecedented eighth world title, trails Verstappen by eight points with just two races left — on the streets of Jeddah on Sunday and at the Abu Dhabi Grand Prix next weekend.
One week on from arguably his toughest and greatest win in Brazil, Hamilton enjoyed one of his easiest.
Formula 1: Max Verstappen given five-place grid penalty at Qatar Grand Prix for 'not respecting' yellow flags
Verstappen had qualified in second originally, but will be replaced on the front row by Alpha Tauri driver Pierre Gasly
The most dramatic Formula 1 title fight in at least a decade further intensified when Horner and Wolff traded barbs at the same time the FIA denied Mercedes' right to appeal last week's non-penalty on championship leader Max Verstappen.
Bottas, set to leave for Alfa Romeo next year, was 0.209 seconds quicker than Alpha Tauri's Pierre Gasly, with championship rivals Max Verstappen and Lewis Hamilton third and fourth.
Verstappen, the winner of the race's previous edition in 2019, finished second and saw his lead in the driver's championship shrink to 14 points, with three races left. The winner of a race gets 25 points.
Hamilton shrugged off that setback by flying through the field from last place to finish fifth from 20th in the sprint.
Brazilian GP: Lewis Hamilton disqualified from qualifying; Max Verstappen fined for touching rival car
Verstappen was fined 50,000 euros by stewards after video taken from the grandstands at Interlagos showed him touching the rear wing of rival Hamilton's car.
Verstappen leads Hamilton by 19 points heading into Sunday's Brazil Grand Prix and the Dutchman looks increasingly capable of denying the Briton the title for the first time since 2016.
Race stewards were investigating whether or not the DRS system - the flap mounted on the rear wing of the car which opens to gain top speed - had exceeded allowed limits.
If Mercedes decide Hamilton needs a fifth engine of the season, it would trigger an automatic penalty of five places on the grid and reduce his chances of claiming a victory to trim or overhaul Max Verstappen’s 19-point advantage in the title race.
Verstappen, who grabbed the lead on the first corner, finished 16.555sec ahead of Hamilton with Perez just over a second further back.
For Bottas, it was a career 19th pole position, bettering the 18 of Rene Arnoux as the driver on most poles without ever winning the world title.
Red Bull's Sergio Perez, racing in front of his home fans at the spectacular Autodromo Hermanos Rodriguez, was fourth at 0.570sec behind his teammate.
Through pulsing race wins, crashes and clashes, the two have crafted F1's best on-track duel in a decade.