The Spectator belongs to Telegraph Group owners the Barclay brothers, who already have an editor's chair to fill on The Daily Telegraph after Martin Newland quit on November 18.
The task of finding a new Spectator editor falls to its chief executive Andrew Neil, who said that Johnson was "in many ways irreplaceable".
Johnson's time as editor of The Spectator was a colourful one, earning it the sobriquet of "Sextator" for the sex scandals that involved the magazine's staff, including its editor.
Johnson said he would be leaving shortly after the Christmas edition has gone to press, and his deputy Stuart Reid would be caretaker editor.
"I want to pay tribute to everyone at the magazine who has helped with its current success, in editorial, production and advertising. For the last six-and-a-half years we have had more fun than seems altogether proper.
"For most of my time here, I have been propelled by their talents, as a fat German tourist may be transported by superior alpinists to the summit of Everest."
According to the Daily Telegraph, he will continue with his weekly column in the paper and also write a column for The Spectator.
Johnson rejoins the Conservative front bench after he was sacked as shadow arts minister by former leader Michael Howard in November 2004, over an affair.
A month earlier, Johnson had been embroiled in a storm caused by an editorial in The Spectator that criticised Liverpudlians for "wallowing in grief" after Ken Bigley was taken hostage and executed in Iraq. He was forced by Howard to take a tour of Liverpool making apologies for the editorial.
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