The win was Verstappen's eighth of the season, and first in America, but one he had to sweat for in front of a sell-out 140,000 crowd.
The 24-year-old Red Bull racer also gave the seven-time world champion, the most successful driver of all time, a single digit salute as the Mercedes accelerated away on a hot and humid Texas afternoon at Austin's Circuit of the Americas.
The new internal combustion engine exceeds the Briton's allocation of three for the season, triggering the penalty.
Seven-time world champion Hamilton is now two points clear of Verstappen with seven races remaining.
Formula One title rivals Lewis Hamilton and Max Verstappen collided and crashed out of the Italian Grand Prix at Monza on Sunday.
The Spaniard halted the session when he smashed head-on into the barriers at the Ascari chicane with just over half an hour remaining.
The news was entirely expected and effectively confirmed when Bottas, 32, announced on Monday his switch to the Alfa Romeo team.
The 23-year-old dominated from pole position to take the chequered flag in the first Dutch GP for 36 years, beating Mercedes' seven-time world champion Lewis Hamilton and Valtteri Bottas.
After some three hours of waiting for the rain to subside, the race started from the pitlane and behind the safety car and was then stopped after completing the two laps required to award half points.
The 40-year-old Spaniard will continue to race alongside Frenchman Esteban Ocon who was handed a fresh three-year deal by the Renault-owned team earlier this season.