The billboard is situated on the side of the GlaxoSmithKline building along the M4 flyover in west London.
Nike say the provocative image is meant to represent the way the Manchester United and England star Rooney celebrates a goal.
A spokesman for Nike said: "His arms are outstretched and his fists are clenched. This position lent itself so well to the flag shape of the ad."
But Nike dismisses claims that the poster, created by agency Wieden & Kennedy, plays on the crucifixion. Nike said: "It's not intended to have religious connotations."
As part of his £5m deal, Rooney posed for three hours in a studio for the image, which is 60ft by 90ft in size.
The image will also appear across the UK on other billboards, in Nike stores and press ads, as well as a centre-spread poster in The Star, The Sun and The Guardian today.
The timing of the poster coincides with the 20-year-old's full return to the England team following injury. He has been named in the starting line-up for England's match against Sweden at 8pm tonight after coming on a substitute in the second half against Trinidad & Tobago.
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