At the start of the year, Rooney - who has more than 4m followers on Twitter - posted on the microblogging site: "My resolution - to start the year as a champion, and finish it as a champion...#makeitcount gonike.me/makeitcount."
Arsenal and England star Wilshere also posted: "In 2012, I will come back for my club - and be ready for my country. #makeitcount.gonike.me/Makeitcount."
But the Advertising Standards Authority today (June 20) upheld a complainant's challenge that both tweets were not "obviously identifiable as marketing communications".
Sportswear giant Nike had tried to argue that the tweets "should be viewed in the context in which they appeared".
The US firm said that Twitter was a "direct channel of communications between two parties", and both players were communicating with Twitter members "who had chosen to 'follow' them".
Nike said that for the "#makeitcount" campaign on Twitter, it had asked Rooney and Wilshere about their goals for 2012, and then left them free to reply or retweet messages around their original tweet.
It said that the campaign could be "objectively viewed as marketing communications" due to the Nike URL that was placed in the body of the tweets.
"We considered the average Twitter user would follow a number of people on the site and they would receive a number of tweets throughout the day, which they may scroll through quickly," said the ASA.
"We noted the [Advertising] Code did not just require ads to be identifiable as marketing communications but that they must be obviously identifiable as such.
"We noted the ad included a Nike URL which directed users to the Nike website and that it contained the hashtag #makeitcount which referred to their new 'make it count' campaign that launched around the same time the tweets appeared.
"However, we considered that the Nike reference was not prominent and could be missed, consumers would not have already been aware of Nike's '#makeitcount' campaign and that not all Twitter users would be aware of the footballers' and their teams' sponsorship deal with Nike.
"We considered there was nothing obvious in the tweets to indicate they were Nike marketing communications. In the absence of such an indication, for example #ad, we considered the tweets were not obviously identifiable as Nike marketing communications and therefore concluded they breached the Code."
The ASA said that the adverts must not appear again and Nike must ensure that its future advertising is "obviously identifiable as such".
Earlier in the year, the ASA cleared Snickers for running a Twitter campaign that involved celebrities such as Katie Price and Cher Lloyd posting several out-of-character tweets, before revealing the line: "You're not you when you're hungry."