St Mary and All Saints Cathedral and other properties had been occupied by Dr Nolbert Kunonga, a former bishop who was excommunicated from the Anglican Communion in 2007 over his support for Robert Mugabe.
The properties were finally returned to the Church of the Province of Central Africa after the Zimbabwean Supreme Court found in its favour.
The court victory was celebrated by a historic thanksgiving service in Harare attended by a thousand worshippers.
The Bishop of Harare, the Right Reverend Chad Gandiya said: "All those five years we were driven from our churches and went into exile, life was not easy but God was with us. We survived and found grace in exile."
He called upon Anglicans to work together in rebuilding the diocese, saying that many of the churches and schools were in need of renovation after years of neglect.
"As we journey from the past, pressing on towards the goal together, there is a lot of work to be done in the area of rebuilding our diocese," he said.
The Primate of the Province, Archbishop Albert Chama, said, "You are going back to your churches to worship God in dignity as it was intended to be. Be strong as you are a testimony to the rest of the church.
"Continue and never relent because wherever we are we say we are learning from the church in Zimbabwe."
A message of congratulations was sent to the Diocese of Harare from the Archbishop of Canterbury, Dr Rowan Williams.
In it, the Archbishop praised the way in which they had persevered through the many difficulties of the last five years.
"You have faced threats of violence and arrest and yet your faith has not weakened, rather it has grown stronger," he said.
"I want to commend particularly the leadership of Bishop Chad Gandiya and Bishop Sebastian Bakare before him, as they have embodied authentic Christian servant-hearted leadership. Through all this, your faith has been a beacon of light to the rest of the Anglican Communion."