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The theologian passed away in London at 1515 GMT on Wednesday, according to John Stott Ministries President Benjamin Homan.
Stott was the former Rector of All Souls Church, Langham Place, in London and was one of the founders of the Lausanne Movement, a worldwide movement of evangelicals.
He was largely responsible for the Movement's two major documents, the Lausanne Covenant in 1974 and the Manila Manifesto in 1989.
Stott was unwavering in his emphasis on the basics of classical evangelicalism – the need for personal conversion, the authority of Scripture and the centrality of Jesus' death for sinners.
However, he was also passionate about the moral and social dimensions of the biblical gospel, including justice for the poor and the care of creation, and was against limiting Christian engagement with the world to evangelism.
Stott retired from public ministry in 2007 but never lost his global influence or interest in the goings on of the world church, and more particularly global evangelicalism.
He was Honorary Chairman of the Lausanne Movement until his death and retained a keen interest in last year's Third Lausanne Congress in Cape Town.
According to close friends, Stott had longed to see the event come to pass and described the document that emerged from the congress, the Cape Town Declaration, as "beautiful and profound".
Although Stott will always be associated most greatly with the Lausanne Movement, he often supported the wider evangelical family, writing the preamble to the constitution of the World Evangelical Alliance (WEA).
International Director of Langham Partnership, Chris Wright, made a touching tribute to his mentor.
"For the vast majority of people whose lives he influenced profoundly, he was simply 'Uncle John' – a much loved friend, correspondent, and brother, to whose prayers we will never know how much we owe," he said.
"Like Moses, he was one of the greatest leaders God has given to his people, and yet at the same time, one of the humblest men on the face of the earth.
"He was, for all of us who knew him, a walking embodiment of the simple beauty of Jesus, whom he loved above all else."
International Director of the WEA, Dr Geoff Tunnicliffe, said Stott would be "greatly missed".
"Uncle John, was a great influence in my own theological development," he said.
"His commitment to biblical orthodoxy, global mission and unity in the body of Christ were foundational in my own spiritual journey."