Whyte said he plans to launch two businesses and will not return to advertising.
McCann's fortunes have taken a recent upturn, so Whyte's departure came as a surprise to some at the agency. However, sources suggested he had kept a low profile internally in recent times.
Brett Gosper, the recently appointed president of the McCann Group EMEA, added that events and dynamics at the agency had changed over the past 18 months. He said: "There was never a plan to get rid of Stephen. My plan when I arrived was to make sure the senior management team was correct, and I have every confidence in Chris."
Macdonald was promoted to managing director in February 2006, having joined the agency as the client services director in 2005.
Whyte was appointed by the network's former European chief, Rupert Howell, in 2004. Howell was replaced by Gosper last summer.