Lewis' resignation will take effect from 18 May, ending a four decade-long career in the Australian Public Service.
Before being appointed as secretary in 2013, Mr Lewis served at senior levels in the departments of defence and finance. Prime Minister Malcolm Turnbull congratulated Lewis on his career and service to the DVA.
"Mr Lewis has performed with distinction as secretary of Veterans’ Affairs and can be proud of his many achievements. Thanks to his stewardship, services to veterans and their families are being significantly modernised and improved, and the transformation program he initiated is driving real change to culture and processes," the Prime Minister said in a statement.
"His leadership of the commemoration of Australian Defence Force service and sacrifice over the Anzac Centenary period was exemplary. It enabled Australians to celebrate and remember the proud history of veterans past and present. I thank Mr Lewis for his dedication and service to the Australian people and wish him the very best for the future."
The Prime Minister also confirmed his intention to recommend Elizabeth Cosson AM CSC to the Governor-General as Lewis's replacement.
Cosson has been the deputy secretary and chief operating officer at DVA since May 2016. Her public service career also includes senior appointments in the departments of health and immigration and citizenship.
Cosson had a distinguished career in the Australian Army, which spanned over three decades. She was the first woman promoted to the rank of Major General and was appointed as a Member of the Order of Australia in 2011 for exceptional service to the Australian Army and the broader Defence organisation. She was also awarded a Conspicuous Service Cross in 2001 for outstanding achievement as the Chief of Staff, Peace Monitoring Group, Bougainville, and in logistic planning and management of the Combat Force of Land Headquarters.
The PM said the appointment of Cosson will coincide with the government achieving gender parity at the senior level of the Australian Public Service.
"As the Department of Veterans’ Affairs marks the centenary of its establishment as the Repatriation Department, I am delighted that it can also celebrate the appointment of its first female secretary," the Prime Minister said.
"With Ms Cosson’s appointment, we have now achieved gender parity at the most senior level of the APS, with nine women and nine men serving as Commonwealth secretaries."
Minister for Veterans’ Affairs Darren Chester said the focus of Cosson's work over the next year will be the department's continued reform and engaging with younger veterans.
"As chief operating officer she has been instrumental in the reform process currently underway and I’m confident that we can continue to deliver an improved level of service," the minister said.
"The focus of our efforts over the next 12 months will be engaging with younger veterans and working to ensure the transition from military service to civilian life is made easier for all concerned. We have made great progress but there is still work to be done and I’m confident Ms Cosson will continue to make a huge contribution to the veteran community."