Congregations will be asked to pray for the country as Britain approaches 29th March.
Archbishop of Canterbury Justin Welby said "life will go on" after Brexit and the nation must rise to the challenge and unite around a common good that cares for the most vulnerable.
A church spokesman said the move would wedge support behind politicians, with healthy conversations taking place to try to ease unrest.
The Synod members urged churchgoers to pray for "all who are in high positions, as it is easier to stand on the sidelines and judge, as we do not have to make the decisions".
Speaking at the meeting of the Church of England's General Synod, he said Britain was facing signs of division "more clearly than for generations".
The Archbishop said: "Today we see signs of division, perhaps more clearly than for generations in peace time, they concern inequality and injustice and they obscure hope for many.
"There is exclusion from the sense of common purpose and of equal rights in our society, politically, economically and socially.
"Life will go on, and God's mission is not stopped by such events, rather we are called to rise to the challenge here and across Europe, where the diocese is particularly affected.
"Brexit has revealed how our politics and society have for many decades not paid sufficient attention to the common good that is shared life in a society in which everyone is able to flourish.
"The pain and exclusion continues in this country. If we do not as a nation pay attention it will cause greater division."
He added: "We hear the prophets tell us that justice must roll down like rivers and righteousness like an ever-flowing stream, the Bible does not do trickle-down economics, a theory long discredited.
"It does rolling rivers of justice, the scriptures call us to solidarity with the poor and to common good.
"The reality of exclusion and division is seen in the difficulty of our political system to build a consensus and find a common path forward.
"How we recover from and heal these divisions may be the biggest challenge that lies ahead of us."
The Archbishop of York John Sentamu said a prayer ahead of Britain leaving the EU.
This would be an open welcome plea to reconnect the fractured state of politics in the nation, working alongside other faith leaders.
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.
Tell us what you think about our news service, what you want and how Premier fits into your news landscape. Take our quick survey!