Kenny’s Convenience Stores – which operates seven stores under the Spar brand – confirmed in a Facebook post they had become aware of the staff member’s involvement in the video.
They said they were treating it “with the utmost seriousness” and the worker has been sacked “with immediate effect”.
They also issued an apology to the family of Mrs McAreavey.
“We acknowledge that the behaviour undertaken was carried out in a private capacity beyond the control of the company however we are treating this matter with the utmost seriousness,” they wrote.
“As a business we do not tolerate or condone offensive or disrespectful conduct from our staff.
“We have advised the staff member that their employment has been terminated with immediate effect.
“We apologise unreservedly for the hurt that this has caused the McAreavey/Harte families, our staff, customers, and the communities we have served for the last 29 years.”
The former employee is believed to be the second person to have been fired over the video, after a Derry firm sacked a man earlier this week.
The video clip, believed to be filmed in an Orange Hall during last month’s Northern Ireland Centenary celebrations, showed several men singing a song about the 27-year-old teacher from Tyrone.
Mrs McAreavey was strangled in her room at the Legends Hotel in Mauritius on January 10, 2011.
The bride, who had married husband John 10 days earlier, was attacked after she returned to her room alone and disturbed a burglary.
No-one has been convicted of murdering the daughter of GAA manager Mickey Harte.
The emergence of the video on social media last week led to widespread condemnation across the political spectrum.
The Orange Order, which branded it “abhorrent”, also launched their own probe into the incident.
On Monday, Justice Minister Naomi Long confirmed she has been in touch with the PSNI Chief Constable Simon Byrne about the incident and it is understood three people who appeared in the video have resigned from the Orange Order.
They have expressed their their "complete shame and regret for their involvement in the incident".
They insisted there was no intent to broadcast the chant on social media and it was "incidentally streamed" on Facebook Live.
One man was interviewed by police investigating the controversial clip after voluntarily attending Dungannon PSNI station on Sunday.
Ms Long also said she understands “at least” one file will be sent to the Public Prosecution Service (PPS) over the video.