Star reader Neil Moran spotted the new area - and large ‘John Lewis & Partners’ sign - in the supermarket on Ecclesall Road.
He said it was an attempt to look like a separate John Lewis store and branded it ‘thoughtless’ and ‘inappropriate’.
John Lewis closed its store on Barker’s Pool at the start of lockdown three in January. In March the company said it would not reopen, with the loss of 299 jobs.
The bombshell move came after it signed a new lease with Sheffield City Council in August last year intended to keep it in the city centre - paying a peppercorn rent - for at least the next 20 years.
That followed almost 20 years of negotiations over its place in a series of redevelopment plans.
Waitrose was also criticised for announcing plans to remove recycling bins from its car park in June. The decision was quickly reversed after an outcry.
Mr Moran, of Endcliffe Rise, said: “The massive ‘John Lewis’ sign over the aisle in Waitrose just isn’t appropriate so soon after the closure of the main store in town. I think that it is thoughtless and shows contempt for the people of Sheffield.
“They have also tried to make that aisle look like it might be part of a John Lewis store, rather than just one of the aisles in Waitrose.
“Waitrose has always sold ‘John Lewis’ homeware goods such as cushions, towels and glassware but they have never branded any of the aisles John Lewis. It seems very thoughtless to do it at this time.
“On the whole, I feel that JL has dealt badly with Sheffield over this whole issue. They were meant to be the centre pin in the regeneration of the city centre. Didn’t we demolish the fire station for them?”
A Waitrose spokesman said: “Like most Waitrose shops, our Sheffield store has always sold a selection of John Lewis products. As part of a national rollout of John Lewis products across our Waitrose shops, we expanded this range earlier this year before we announced the proposed closure of John Lewis Sheffield.”