Mr Wilson will leave his executive role immediately, the FTSE 100 insurer said, but remain with the group until April 2019 while a successor is appointed.
Chairman Sir Adrian Montague will assume executive responsibilities while Aviva launches the hunt for a new CEO.
He will chair a committee of three executive directors: UK insurance chief executive Andy Briggs, chief financial officer Thomas Stoddard, and international insurance chief executive Maurice Tulloch.
The move follows Mr Wilson’s decision in March to join the board of rival asset manager BlackRock, which angered some shareholders.
Aviva said it was time for “new leadership” after five years under Mr Wilson in which he led a turnaround which the company said was now complete.
“He leaves the group in a far stronger state than when he joined,” said Sir Adrian. “Aviva is now financially strong and delivering solid earnings growth.
“There is much further to go in accelerating our strategic development and enhancing shareholder value. We have agreed with Mark this is the right time for a new leader to ensure Aviva delivers to its full potential.”
Aviva will start the search for a successor immediately. The process is expected to take four months.
Mr Wilson said: “When I joined Aviva, the company was in poor health. Aviva is very different today.
“I have achieved what I wanted to achieve and now it’s time for me to move on to new things.
“It has been an honour to lead Aviva through this period of immense change. I am happy I leave the company in a strong position from which it can thrive.”