Viewers in the south of England and Wales missed the final six seconds of the ad, which showed Cristiano Ronaldo running up to take a free kick and included an endframe with Nike's logo and website address.
The UK's largest commercial broadcaster has "apologised unreservedly" to Nike and blamed a technical problem.
A Nike spokesman said: "We have discussed this with ITV and although we're disappointed it happened, it seems it was technical error, not human error. We've agreed a form of compensation with them that we're happy with."
WPP's Mindshare is the media agency for both Nike and ITV, and was keen to downplay the affair.
Nike's epic three-minute new World Cup TV ad features Wayne Rooney, Cristiano Ronaldo, Ronaldinho, Fabio Cannavaro and Didier Drogba.
It is not the first transmission problem ITV has suffered in relation to football coverage and advertising.
In February 2009 it angered viewers watching an Everton-Liverpool FA Cup tie when it aired a Tic Tac ad instead of the live extra time action of Everton's winning goal. Tic Tac later recreated the goal in a viral film to apologise to fans.