Police have confirmed the crash took place near the German city of Bielefeld at 15:35 CET and the player was pronounced dead at the scene.
Malanda, 20, was due to fly to South Africa on Saturday evening along with the rest of his Wolfsburg team-mates for a training camp ahead of resuming their Bundesliga campaign after the winter break.
The Belgian had joined Wolfsburg in 2013 from Zulte Waregem and was also on the books at Anderlecht and Lille in his earlier years.
Malanda last played for Wolfsburg in their 2-1 win over Cologne on December 20. He had represented Belgium at every youth level up to and including the Under-21 side.
"We are all deeply upset," said Wolfsburg managing director Klaus Allofs.
"We all loved him. He was the good spirit of our team and a fun-loving person. In addition, Junior was an excellent football player who stood at the beginning of his development.
"We cannot still believe that he is no longer with us. Our thoughts are in these difficult hours with his family and his relatives."
A statement from the Belgian Football Association read: "The football world today lost a great talent. Junior Malanda lost his life this afternoon, at the age of 20.
"The Belgian Football Association extends its sympathy to family and friends."
Team-mate and fellow Belgium youth international Kevin de Bruyne took to his official Twitter account to show his grief.
Alongside a picture of himself and Malanda, he posted: "So strange to hear your friend in the morning and then hear this news. Lost a great friend way too early. RIP my friend @JuniorMalanda."
Fifa president Sepp Blatter said: "Shocked and saddened by the tragic death of Junior Malanda. Soccer loses a great talent. My thoughts are with his family."