Brexit would "profoundly" affect the country's future, but its citizens should look to examples from Britain's past for a route towards social harmony, the Most Rev Justin Welby said in his address to the nation.
His message comes after former Ukip leader Nigel Farage criticised as "negative" the Archbishop's Christmas Day sermon, which did not mention Brexit.
The 60-year-old said: "Last year, we made a decision that will profoundly affect the future of our country - a decision made democratically by the people.
"The EU Referendum was a tough campaign and it has left divisions.
"But I know that if we look at our roots, our history and our culture in the Christian tradition, if we reach back into what is best in this country, we will find a path towards reconciling the differences that have divided us.
"If we are welcoming to those in need, if we are generous in giving, if we take hold of our new future with determination and courage - then we will flourish."
He cited Dick Howard, the Second World War-era Provost of Coventry Cathedral, who called for a more "Christ-like world" following the bombing of the area in 1940, and praise the city as an example of "Britain at its best".
Being hospitable to strangers and living well together are the foundations of British values and traditions and can make the UK "a beacon of hope" in a "troubled world", he said.
The Archbishop's new year message was broadcast on BBC One on Sunday.