McDonald worked with the new Rovers boss during their time together at Bolton. As a result of McDonald's appointment, Paul Ince's assistant Ray Mathias and first-team coach Archie Knox have left Ewood Park.
Leeds will receive compensation for McDonald, who joined Leeds as first-team coach in February, and Gary McAllister has indicated that he will not rush into naming a replacement.
McAllister, who has Steve Staunton as his assistant, said: "I'm disappointed he's gone but it's not necessarily crucial. Steve and I have done a fair bit of coaching over the years so we're fine on that score."