All three were accused of not following yellow flag rules near the end of qualifying. Bottas, who had qualified third, was penalized three starting sports. Sainz was not penalized.
Red Bull was mystified by the grid penalty for Verstappen, who lost any chance to challenge Hamilton for the win when he was penalized. Red Bull principal Christian Horner criticized the penalty when it was handed down.
Alonso of Spain finished third behind The Netherlands' Max Verstappen and Lewis Hamilton. (Hamad I Mohammed - Pool/Getty Images)
"We’re really struggling to understand it," Horner said. "That’s a crucial blow in this world championship for us."
Despite the penalty, Verstappen needed only five laps to recover and drive back to where he was originally slated to start.
"Our starting position was a bit compromised," Verstappen said. "I know it's going to be difficult to the end but I think that's nice. It keeps it exciting."
But he said he was ready for the challenges ahead in Saudi Arabia and the finale in Abu Dhabi.
"I feel good," he said. "It's going to be tight."
Hamilton, winner of four straight titles, has all the momentum now. The British driver is seeking a record eighth F1 title, which would move him past Michael Schumacher.
"I'm feeling really good, I'm really, really happy with the car," Hamilton said. "I feel fitter than ever, so that's a positive."
Fernando Alonso of Alpine finished third for his first podium since 2014. He was aided by the pre-race penalties to Verstappen and Bottas, which moved the Spaniard up to third on the starting grid.