The 19-year-old midfielder suffered sprained and partially torn ligaments in his right knee after a challenge with Dortmund defender Sokratis Papastathopoulos as Wolfsburg fell to a 2-0 defeat at Signal Iduna Park in the DFB-Pokal semi-final.
Malanda could now face two months on the sidelines, meaning that he will play no part in Wolfsburg's Bundesliga run-in as they seek a top-four finish.
"He's been lucky in that it's not the cruciate, which we feared, but it's still unfortunate for him," Wolfsburg coach Dieter Hecking told the club's official website.
"It's a pity but at least he will be fighting fit for the start of pre-season.
"He was one of our most active players (against Dortmund). He's a young lad but he showed that he's already capable of assuming the responsibility."
Malanda - who spent the first half of the season on loan at Zulte Waregem - has represented Belgium at Under-21 level.
He had been tipped to be a surprise inclusion in Marc Wilmots' Belgium squad for the FIFA World Cup in Brazil later this year, but this setback is likely to scupper those hopes.
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