The ruling follows tweets by Manchester United footballer Wayne Rooney and his Arsenal rival Jack Wilshere, posted at the request of the sportswear firm.
The Advertising Standards Authority said that the messages did not make clear they were "identifiable as marketing communications".
It marks the first time the ASA has acted against a Twitter-based campaign.
The authority said it had intervened after receiving a single complaint earlier this year about two tweets - one from each of the sportsmen posted to their personal accounts.
Wayne Rooney's tweet read: "My resolution - to start the year as a champion, and finish it as a champion...#makeitcount gonike.me/makeitcount".
Jack Wilshere had posted "In 2012, I will come back for my club - and be ready for my country gonike.me/Makeitcount".
Rooney has close to 4.8 million followers on his account. The offending tweet - posted on 1 January - has not been deleted.
Wilshere's account was suspended over a fortnight ago after he received personal abuse about an unrelated issue. A spokesman for Arsenal said its midfielder had about 1.3 million followers.
The ASA said the Nike mention in Jack Wilshere's post was "not prominent"
The complainant challenged whether the tweets were "obviously identifiable" as adverts.
Nike responded that the presence of its web address alongside a hashtag with its marketing campaign strapline distinguished the tweets from other personal posts by the players. It added that both sportsmen were well known for having being sponsored by the company.
But the ASA said the elements did not make the tweets "obviously identifiable" as adverts, bearing in mind that many Twitter users scroll through a variety of messages at speed. It added that not all of the social network's users would have been aware of the "make it count" campaign, or the footballers' relationship with Nike.
It suggested that in future firms should add #ad or some other clear indication that a message had been paid for.
"This is relatively new territory for us as a regulator," ASA spokesman Matt Wilson told the BBC.
"People are experimenting and using Twitter to reach consumers, but the same advertising rules apply. It's an ongoing process and this illustrates the care firms must take."
He added that the authority was "relatively relaxed" about the fact that Rooney's tweet had not yet been deleted, bearing in mind it was not at the top of his feed, but added that it expected it to be removed later.