Neville Isdell, the former Coke and BT executive who was appointed to the top role ahead of Heyer, said: "In discussions over the past week, Steve and I have looked at how he could best realise his personal goals given my election as chairman and chief executive officer of this company.
"We agreed that Steve could best realise his aspirations by pursuing opportunities outside of the company."
The soft drinks giant has stressed that Heyer's departure is by mutual consent and that he will continue in the role for several months to ensure an "orderly transition".
Heyer had hoped to fill the role of CEO and chairman as the only internal candidate after the previous postholder Douglas Daft announced his retirement in February.
Other contenders for the position are understood to have included James Kilts, chairman and chief executive of Gillette.
If you have an opinion on this or any other issue raised on Brand Republic, join the debate in the .