Left-back Malacia joined United from Feyenoord in 2022 for a deal reportedly worth around 13 million pounds ($15.56 million) plus another 1.7 million pounds in add-ons.
The 25-year-old made 22 Premier League appearances in his first season but missed the entirety of the 2023-24 campaign due to a knee injury.
"I'm happy to be here. Finally playing good football again. I am coming off a long injury, but by now I am fit and know that my time will come again," Malacia said in a statement.
"In every tough period there are also positive elements and in this case that is that I have become much stronger physically and mentally. I have more patience, I am more mature, know my body better and things like that."
PSV lead the Dutch top-flight's standings with 50 points from 21 matches, two points ahead of Ajax, who have a game in hand.