The major provider, which has 33m customers, said Mr Wilson would leave immediately and be on full salary and benefits on gardening leave for six months.
A company spokesman said: “Mark Wilson will be placed on garden leave for six months with effect from 9 October 2018. During this period he will continue to receive his salary and contractual benefits.
“At the end of this period, the company will make a payment in lieu of notice of six months' basic salary, pension entitlement and contractual benefits, in monthly instalments, over the remainder of Mark Wilson's contractual 12 month notice period.
“Mark Wilson's employment will therefore terminate on 9 April 2019 (the "Termination Date"). Mark Wilson will be required to mitigate his loss during the period following the Termination Date until 9 October 2019, by seeking alternative employment or engagement.”
Mr Wilson will also be given up to £10,000 towards any legal fees connected with his departure, Aviva said.
He will be entitled to a pro-rated bonus for the 2018 financial year but no bonus will be payable for the company's 2019 financial year.
While the company has seen financial improvement it has been hit by a number of technical problems over the past 12 months. Its adviser site suffered issues when some advisers struggled to submit business at times and its replatforming process came unstuck earlier this year with delays affecting the changeover.
Despite the problems, the provider reported growth in its platform assets in its latest report - showing net fund inflows of £2.2bn.
The search is now under way for a replacement - both internally and externally - for Mr Wilson.
While the hunt for a replacement takes place Aviva chairman Sir Adrian Montague take over Mr Wilson’s chief executive role.
Sir Adrian said Mr Wilson had helped turn round the business financially and the company said this turnaround had been “successfully completed” and it was time for “new leadership.”
Sir Adrian said: “The board would like to thank Mark for what he has achieved in his six years at Aviva. He leaves the group in a far stronger state than when he joined. Aviva is now financially strong and delivering solid earnings growth.
"There is much further to go in accelerating out strategic development and enhancing shareholder value. We have agreed with Mark it is the right time for a new leader to ensure Aviva delivers to its full potential."
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 is time for me to move on to new things.”