The 20-year-old was en route to meeting up with the squad for their flight to Cape Town later in the day when the car he was a passenger in started to swerve, crashed into a tree and flipped over several times.
No other vehicle was involved, Bielefeld police added.
“We are deeply shocked and cannot put our consternation into words,” said Wolfsburg sporting director Klaus Allofs in a statement. “We all loved him.
“He was a fun-loving person. Above that he was an outstanding player who was at the start of his development. Our thoughts these difficult hours are with his family and friends.”
Police said the driver and one other passenger, also both 20-year-old Belgians, were injured. The accident occurred amid strong winds and heavy rain on the North Rhine-Westphalian motorway.
“So strange to hear your friend in the morning and then hear this news. Lost a great friend way too early. RIP my friend,” said Wolfsburg team mate and fellow Belgian Kevin De Bruyne on his official Twitter account.
Danish forward Nicklas Bendtner wrote: “Not only a great player but a great person. My thoughts and prayers will always be with you and your family, brother. You will always be remembered.”
Malanda, who did not win a senior cap, joined Wolfsburg in 2013 and had a spell on loan at Zulte Waregem.
He played a total of 17 league games for Wolfsburg, 10 this season, scoring two goals.
“Belgian football has lost one of its greatest hopes,” said national coach Marc Wilmots. “My thoughts are with the family and friends of Junior Malanda.”
The Bundesliga resumes on January 30.