The ancient and iconic city will be flooded because the Mediterranean Sea is forecast to rise by up to 140cm before 2100, according to the research.
The same rise in sea level is predicted to swamp a 176-mile long coastline in the north Adriatic and parts of the west coast of Italy, because of greenhouse gas emissions.
The report, published in Quarternary International, claimed up to 5,500km2 of coastal plains will be flooded before 2100.
“The subsequent loss of land will impact the environment and local infrastructures, suggesting land planners and decision makers [should] take into account these scenarios for cognizant coastal management,” said lead author Fabrizio Antonioli.
“Our method developed for the Italian coast can be applied worldwide in other coastal areas expected to be affected by marine ingression due to global climate change.”
The study, by the ENEA (the Italian National Agency for New Technologies, Energy and Sustainable Economic Development), looked at how flooding had affected millstone quarries to predict the possible rise in sea levels.
Millstones are circular stones that were mined to grind grain in the Stone Age pre 2,000 BC.
“We integrated historical sources, aerial photography, field surveys and palaeo sea-level modelling to investigate a number of millstones quarries with the aim of assessing the intervening sera level change that occurred since the quarries were abandoned,” added Mr Antonioli.
The research also said sea levels rose by just 32cm over the past millennium.
The team also believes 33 areas across Italy are particularly at risk from the predicted rise.
This includes the coastline between Trieste and Ravenna, the Parc Delta del Po Veneto where hundreds of flamingos live, Verslia in Tuscancy on the west coast, and Fiumicino in Lazio.
About 86 million people in Europe – around 19 per cent of its population – are estimated to live within 10km from the coastline. Around 75 per cent of the Italian population are estimated to live within 10km of the coast.
A separate study released earlier this year suggested global warming could cause sea levels to rise higher than the height of a three-storey building.