Mekies was named Scuderia AlphaTauri team principal in anticipation of incumbent Franz Tost retiring at the end of the season.
That triggered a protracted back and forth between Ferrari and Red Bull over how the Frenchman would transition into the new role.
That was complicated by the fact he held a contract with Ferrari.
A solution has now been found, with Mekies absent from this weekend's Belgian Grand Prix.
“Laurent Mekies' time at Scuderia Ferrari comes to an end this week,” the Italian team announced via a statement.
“The racing director will not be in Belgium and he leaves the Prancing Horse after four and a half seasons, during which time the team took seven wins.
“The entire team thanks him for his great contribution during those years.”
Ferrari has announced Diego Ioverno as Mekies' replacement.
“As from the Belgian Grand Prix, part of Laurent's duties on the pitwall will be carried out by Diego Ioverno, who takes on the role of sporting director,” the Ferrari statement confirmed.
“He will be responsible for all sporting matters, as well as liaising with the FIA (Federation Internationale de l'Automobile).
“Ioverno is a veteran member of the Scuderia having worked in Maranello for the past 23 years.
“Along with his colleagues on the pitwall, Matteo Togninalli, Head of Track Engineering and Ravin Jain, Race Strategist, he will report directly to Team Principal, Fred Vasseur.”