The roll is in a "remarkably unused condition", say Whyte`s auctioneers.
German soldiers` helmets, minefield warning flags and a police dagger are among the other items going under the hammer on 17 September.
A private Irish collector had assembled the collection over a 25-year period and it was fascinating that the toilet paper remained intact, said Whyte`s Head of Collectibles Stuart Purcell.
It was one of the more bizarre artefacts he had come across, added Mr Purcell.
"We had a German World War Two helmet on sale in March which sold for 10,000 euros and the guy whose collection it is was one of the bidders," he told the BBC.
"The private collector`s raison d`etre in the early days was to try and collect the kit of the average World War Two soldier - everything from what he used for cleaning his gun to his butter dish.
"It is fascinating that someone in 1945 would say: `We will put that toilet paper aside because someone will find that interesting in the future.`
"You would have thought it would have been used during the war."
A WW2 German Luftwaffe helmet is among the items in the auction
`Sinister`
Mr Purcell acknowledged that some people would think the concept of collecting Nazi militaria was "sinister" but said their retention had historical significance.
"The people who collect these items are usually serious collectors," he said. "For some people though it is like collecting stamps.
"If they weren`t still collecting it, in a generation`s time people would say we don`t have anything to show as nobody bothered to collect it."
The private collector selling the toilet paper had collected some 30 German helmets dating back to World War One, said Mr Purcell.
"There are WW2 paratrooper helmets and a number of Waffen SS helmets, which are very rare," he said.
"We also have a Nazi railway police dagger which is rare and is on at 1,500 to 2,000 euros."
German minefield warning flagsWhyte`s auction house
A selection of German minefield warning flags are also up for auction
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