The Columba Declaration paves the way for future joint working between the two churches.
It came after the moderator of the General Assembly of the Church of Scotland addressed the synod.
It is believed to be the first time a serving moderator has been invited to speak at the Church's governing body.
The Right Rev Dr Angus Morrison told the gathering in London:  "The strengthening of the bonds which already exist between us can only serve the 'advance of the Gospel' which is our united desire and aim."
The declaration sets out how members and clergy will be allowed to worship and exercise ministry in each other's churches.
It will also offer opportunities for congregational partnership, formal and informal, where there are churches close to each other.
Members voted 243 votes to 50 to approve the document at the synod.
The Bishop of Chester, the Right Reverend Dr Peter Foster, who co-chaired a study group which prepared the agreement, said:  "As our country has become more secular, we find ourselves drawn together as we face common problems, and opportunities.
"For all the ways in which our recognition and calling as national churches has had very different histories and legal structures, we have found that we have more in common, in our common tasks in mission, than we might have been led to suppose."
The report will now go to the General Assembly of the Church of Scotland in May for approval.
The Church of England's general synod has backed a report proposing a historic agreement with the Church of Scotland.