Gesser, who joined the Eredivisie club three years ago, was due to be part of the under-17 set-up in the coming season.
A minute's silence was held ahead of Ajax 1 and Jong Ajax matches on Sunday (AEST), with flags flown at half-mast at the training centre.
A club statement read: "Ajax has received the terrible news that Noah Gesser has passed away.
"The sixteen-year-old youth academy player was killed in a car accident with his brother on Friday evening.
"Ajax is deeply moved by this tragic event. The club wishes Gesser’s loved ones strength in the coming time in dealing with this immeasurable loss."