The club said Nike immediately stopped production after relatives of those killed in the tragedy expressed concern that their loved ones could be abused for marketing purposes.
This week, the image of a Nike soccer with the number “96” and the eternal flame appeared.
“We would like to apologize from the bottom of our hearts to all those who were offended by these designs”.
The hype surrounding Nike’s LFC products has increased in recent weeks, partly fuelled by “leaked” design images.
Nike has won a high-profile lawsuit to secure a deal in which the US company will produce the Reds’ jerseys starting next season.
At no point did the ball make it to the sales floor.
The ball also carried the number 96 – an allusion to the 96 innocent men, women and children who died after the tragic terrace fall at the 1989 FA Cup semi-final in Liverpool with Nottingham Forest.
Among the images shared online was a red football with the Nike Tick logo and a liver bird above the letter “LFC”.
The prospect of a commodity with a reference to the ’96s caused concern among relatives of the disaster victims and survivors.
The number had the symbolic eternal flame on each side.
Lou Brookes, whose brother Andrew died as a result of the tragedy, was one of several relatives who wrote to Liverpool FC asking for an explanation.
Ms Brookes said: “My brother is not a brand. Our 96 are not a brand.
“Our 96 did not die to fill other people’s pockets or to make a living.
Ms. Brookes questioned how such a design had been approved.
“My brother will not be used to make money for others. Enough is enough now. I don’t want my brother to be part of anything that makes money for anyone, and I mean for anyone.
In response to the concerns, Liverpool FC said there had been a “mistake” in the design process and as soon as the club learned about it, the representatives contacted Nike.
It is assumed that Nike reacted quickly and stopped production of the football immediately.
On Twitter, the Hillsborough Survivors Supporters Alliance added: “The 96 are not numbers, they are individuals, they had lives, they have families, they should not be used as a brand to sell goods. Nike, this should not happen”.