In a service rich with music and prayer the Pope said there should be more focus on what unites Christians.
"So many past controversies between Christians can be overcome when we put aside all polemical or apologetic approaches, and seek instead to grasp more fully what unites us," said the Pope.
"We need to realize that, to plumb the depths of the mystery of God, we need one another, we need to encounter one another and to challenge one another under the guidance of the Holy Spirit, who harmonizes diversities and overcomes conflicts," Francis continued.
He then went on to greet some particular visitors attending the service.
"I offer a cordial and fraternal greeting to His Eminence Metropolitan Gennadios, the representative of the Ecumenical Patriarch, to His Grace David Moxon, the personal representative in Rome of the Archbishop of Canterbury," said the Pontiff.
The Eastern churches and the Roman Catholic Church split nearly 1,000 years ago, and full reunion of the two is unlikely. However, relations have warmed notably in recent years.
The Anglican church split from Rome in the 16th century and Anglican ordination of women is a thorny issue between the two Churches, with the Vatican firmly opposed to female priests, and attempts by Francis' predecessor Benedict to woo disaffected Anglicans back to Catholicism has caused more friction.
Francis was inaugurated as the leader of the world's 1.2 billion Catholics on March 19, 2013 following Benedict's abdication, and just two days before Justin Welby became Archbishop of Canterbury, officially taking over from Rowan Williams as head of the 80-million-strong Anglican Communion.