Marc, who had already wrapped up a second straight MotoGP crown, set a new record for wins in a season with his 13th, while his 18-year-old younger brother clinched the Moto3 crown.
It means they are the only brothers to hold titles in the same season and it can only be a matter of time before they are direct rivals in the top echelon of the sport.
Alex, who will be promoted to the Moto2 class next season, finished third in the final race, enough to hold off Australian Jack Miller, who won in Valencia, by just two points.
He then watched as Marc overcame tricky conditions to round off another triumphant season on his Repsol Honda with an emphatic victory.
He started from fifth on the grid after a crash in qualifying Saturday, but quickly worked his way through the field.
Marquez eventually took the lead on the 11th lap and had opened up a near four-second advantage by the time he took the checkered flag from Italian legend Valentino Rossi, who clinched second in the title race.
Marquez's teammate Daniel Pedrosa took the final spot on the podium, while Andrea Dovizioso held off his Ducati teammate Cal Crutchlow for fourth.
Marquez, who tied Mick Doohan's 1997 record of 12 runs in the previous round in Malaysia, said he had been inspired by his brother's earlier triumph.
"The truth is I am very, very happy. During the race at times I was thinking of my brother and thought I had to do well," he admitted.
The 18-round season has proved an all-Spanish affair at the top of all the categories, with Esteve Rabat having already clinched the Moto2 crown.