United have agreed a £13 million fee for 22-year-old left-back, matching a bid which had been made by Lyon.
The deal hit complications after Malacia's decision to switch agents but sources have told ESPN the problem has now been resolved and the transfer should be completed in the coming days.
Manager Erik ten Hag is hopeful of having the Netherlands international in his squad in time for the start of the preseason tour of Thailand and Australia on July 8.
Sources have told ESPN that United have also held positive talks with Ajax over a deal for Lisandro Martinez.
The 24-year-old, who can play in midfield or defence and is also wanted by Arsenal, is valued at around £43m but Ajax have signalled they may be willing to compromise over the fee.
Arsenal have had two bids knocked back for Martinez giving United the opportunity to work towards their own agreement.
Old Trafford bosses have also enquired about signing winger Antony but Ajax have so far stuck to their valuation of £70m and United would not be interested in that price.
An initial fee of £56m has been agreed but there are still a number of details to work through, including the payment structure, performance-related add-ons of around £15m and personal terms.
United had hoped De Jong would be their first signing of the summer but sources have told ESPN it is more likely that Malacia is the first new player through the door under Ten Hag.
Ten Hag's first game as manager will be against Liverpool in Bangkok on July 12.