In a last minute debate at the meeting in York members discussed how Britain had been affected by the vote to leave the union.
The British public voted by 52% to 48% to leave the European Union in June.
The Archbishops' of Canterbury and York had called on the Synod to "unite in the common task of building a generous and forward looking country".
Moving the motion the Archbishop of Canterbury, Justin Welby, said: "Although it would be easy to be either utopian, or cataclysmic and apocalyptic, I think that Synod would be deeply mistaken to veer in either direction
"The result has released a latent racism and xenophobia in all sectors, and challenges the prevailing consensus of tolerance and acceptance, thus threatening other areas of welcome liberalisation.
"This is a time for remembering the authority and power of God, revealed in Jesus Christ, and of the good news that we have in our hands for all people in this land. All round the world Christians suffer and yet trust. We can do no less. We are to be led by our theology, which must define our politics, our fears and our hopes.
"The clearest inspiration to those outside the church, the best way we will communicate, the way we bring hope in anxious times, is to be a holy community, and one which is recognised in its conduct as manifestly holy.
"That must mean that we keep the needs of the poorest in this country and around the world at the front of our minds. We must manage our own disagreements, whether over sexuality or other matters, with transparent love and delight, and not with words and actions that discredit the hope of unity. And we must be renewed in joyful and boundless love for each other and neighbor - expressed in action, shown in worship and prayer."