Ms Harris conceded she had told another employee the customer was arrogant, and offered to write a letter of apology.
However, she denied she had called the customer an "arrogant p****" and said she was not racist.
Earlier this year the Employment Relations Authority found the incident was one of serious misconduct and The Warehouse had carried out a proper investigation.
However, the authority found the decision to dismiss her was not fair or reasonable, given Ms Harris' good past track record and the fact she believed she was carrying out her proper duties.
The ERA did not award any remedy because of her contribution to the situation.
The authority's decision has since been challenged by both parties at the Employment Court.
The Warehouse Limited challenged the authority's finding that Ms Harris' dismissal was unjustified and Ms Harris challenged the conclusion that she was to be awarded no remedies.
In his decision, released today, Judge Graeme Colgan found Ms Harris was dismissed unjustifiably.
He said it was improbable Ms Harris had used the phrase alleged.
Judge Colgan ordered The Warehouse Limited reinstate Ms Harris to the role of loss prevention officer, or to a job no less advantageous to her, at the Kaikohe store in Northland or a store closest to the Kaikohe store that had a staff vacancy.
Ms Harris was required to undertake paid customer service or loss prevention officer training before resuming her duties.
The Warehouse Limited was also ordered to pay Ms Harris $4000 in compensation.
Ms Harris, who has been a security worker for 25 years, said she was pleased with the court's decision and was looking forward to getting back to work.
"It has been a long track going through this process from day one, it hasn't been easy ... I can't wait to get back to what I have always done and the work I really enjoy."
The Warehouse Limited was disappointed with the Employment Court decision, public relations manager Joanne Fullam said.
"We are disappointed with the outcome of the decision and we will be appealing aspects of it."
First Union retail and finance secretary Maxine Gay said it was beyond belief that a respected, long term worker was dismissed in this way.
"I am pleased that justice has been done," she said.