The campaign was due to place the Manchester United football player's image on thousands of bottles and cans of Coke Zero, the brand's no-sugar variant.
Coca-Cola today confirmed the promotion had been cancelled, as it did not deem it "appropriate" due to the allegations surrounding the striker's personal life.
An official statement from the soft drinks manufacturer said: "Last month we amended our marketing plans on Coke Zero. Given the situation at that time, we did not feel it was appropriate to run an on-pack promotion featuring Wayne Rooney.
"Our relationship with Wayne Rooney is ongoing. We are currently working with Wayne on Coke Zero Street Striker – an award-winning programme which, over the past three years, has encouraged thousands of young people to get involved in football."
Rooney's deal with Coke is understood to be worth more than £500,000 a year and is in addition to further sponsorship deals with sportswear firm Nike and games manufacturer EA Sports.
Reports in the tabloids at the beginning of last month claimed Rooney had paid up to £1,200 a night to an escort girl.
All three sponsors had initially insisted that the allegations are a personal matter for Rooney and his family. No official statement has come from the Rooney camp.
At the beginning of September, Coca-Cola issued a statement to the press insisting it would not drop the star from his sponsorship deal.
The statement said: "This is a private matter for Wayne Rooney and his family. We will be making no further comment at this time."
Both Nike and EA Sports released similar statements. Nike said: ""This is a private matter for Wayne and his family and we have no further comment to make at this time. We have worked with Wayne for seven years and he continues to be a Nike athlete."
This view was echoed by an EA Sports spokesman who said: "This is a personal matter and we respect Wayne and his family's privacy. We have worked together for six years and Wayne continues to represent EA Sports. We will be making no further comment at this time."
Rooney earns an estimated £5m a year, £100,000 a week, solely from his Manchester United wages. His 2008 wedding to Coleen, his childhood sweetheart, further boosted the footballer's fortune when Hello! magazine paid the couple £1.5m for the event's photo rights.
The 24-year-old's wages plus his endorsements have catapulted him into the Sunday Times Rich List, which this year reported he had earned £33m.
Rooney has also signed a deal with Harper Collins, reportedly the biggest UK sports book deal in publishing history. The deal includes a £5m advance plus royalties for a minimum of five books over a 12-year period.
The Manchester United and England striker put in a lacklustre performance in this year's Fifa World Cup in South Africa, where he failed to score a single goal. The England team exited early, ahead of the quarter-finals, to criticism from the press and public alike.
His wife Coleen Rooney has forged her own career and has promoted Littlewoods and, up until 2008, was the face of supermarket giant Asda.
In February, Rooney starred in an advertising campaign for Coca-Cola brand Powerade.
In the advertising campaign, a shirtless Rooney, fuelled by Powerade, took on a shirted Wayne fuelled by water, in a one-on-one skills and endurance duel. The ad was created by Mother.