The 20-year-old Spaniard (Repsol Honda), who also won in Germany last time out, earned his third triumph of the season ahead of Stefan Bradl (Repsol Honda) and Valentino Rossi (Yamaha) to extend his lead at the top of the championship standings.
He now has 163 points after nine rounds, with his countryman Dani Pedrosa (Repsol Honda) second with 147 points after finishing fifth today and another Spaniard, defending champion Jorge Lorenzo (Yamaha), a further 10 points back in third after a sixth-place finish.
As well as breaking two-time former world champion Freddie Spencer's record of being the youngest MotoGP rider to win successive races, Marquez also became the first rookie to win at Laguna Seca.
German Bradl was also celebrating a first on Sunday.
Having earned pole position yesterday following a crash by Marquez, the 23-year-old ensured he did not waste the opportunity as he claimed his maiden premier class podium finish having previously never managed better than fourth.
Italian Rossi held on for the final rostrum spot - his third in succession - ahead of Alvaro Bautista in fourth.
Britain's Cal Crutchlow was seventh on his Yamaha Tech 3 and he slipped to fifth in the overall standings, a point behind Rossi.
The MotoGP season now has a summer break before resuming at Indianapolis in mid-August.
Marquez admitted the win had taken him by surprise.
"Before I came here, I was expecting to struggle more," he told motogp.com. "From the TV, this circuit looked so tricky. Since FP1 I have felt so good. Next time I'll be able to learn where all of the bumps are and everything - yesterday [Saturday] I found a new bump, when I crashed at turn six!
"Anyway, today [Sunday] in the race it was so good."
He added: "I'm very, very happy because it's a new circuit and I've got 25 points. I'm very happy because it's great to go into the summer break with this result."