The 16-year-old son of seven-time world champion Michael Schumacher posted a winning time of 30mins 59.920secs over the 18 laps at the Oschersleben track, between Hanover and Berlin.
His Van Amersfoort Racing team-mate Joey Mawson, 18, of Australia finished second at 0.518secs back.
The next round of racing will be held in Austria at the start of June.
“Of course, I’m over-joyed, my first weekend of racing couldn’t have gone any better,” beamed Schumacher, who celebrated his victory by spraying champagne he is not yet old enough to drink.
“We had a good start, because I still had fresh tyres and things went well from there, it only got a bit close at the end.
“All in all, I am completely happy over the start of the season and I am looking forward to the next race.”
Having started second on the grid, Schumacher Jnr led from the front living up to the famous name by controlling the race without any mistakes.
His place on the podium caps a successful weekend for the German, who won the best rookie title on his debut behind the Formula Four wheel when he finished ninth on Saturday despite starting 19th on the grid.
Schumacher Jnr then finished 12th on Sunday morning before winning the afternoon’s race.
After a successful karting career, Schumacher Jnr has signed for the Dutch Van Amersfoort Racing team in Europe’s ADAC Formula Four season, which runs until October.
With Michael Schumacher still recovering from a serious head injury suffered during a skiing accident in December 2013, his father Rolf Schumacher was at Oschersleben to watch his grandson race.