A statement on the Ajax website confirmed Arsenal’s move for the 16-year-old striker, described as “a great talent” by his former academy boss Wim Jonk.
Malen had earlier posted to social media a picture of him signing a contract, watched by Arsenal’s transfer negotiator Dick Law.
Ajax’s statement said the Holland youth international had chosen to leave despite the offer of a new deal.
Jonk, head of youth development, said: “Donyell is a great talent. It is extremely unfortunate that he is leaving Ajax.
“We have made him an excellent offer and presented a clear development plan. If the player still makes another choice, it is disappointing.”