The “extraordinary” discovery came after authorities were alerted to illegal excavations by tomb raiders near the ruins of the ancient city in August last year.
Secret tunnels dug by criminal artefact hunters led researchers to a stable buried north of the Pompeii archaeological park.
The site’s directors said the horse was likely to have been owned by a wealthy family and used in military parades.
It was discovered amid the remains of a villa outside the city walls, in an area called Civita Giuliana, and is the first horse unearthed at Pompeii.
Archaeologists made a cast of the animal by injecting plaster into the cavities where its body lay before it disintegrated.
Experts have used the same technique to recreate the final poses of Pompeii’s human victims, who were swallowed by lava after Vesuvius erupted and destroyed the ancient Roman city in AD79.
The horse stood at just under five feet tall, making it smaller than a typical modern-day horse but surprisingly large for its time.
Fragments of an iron and bronze harness were found near its head, suggesting it had been used in parades.
The park’s directors described the remains as an “extraordinary find”.
Archaeologists also unearthed the grave of a man who died following the eruption, as well as household artefacts including a jug, kitchen utensils and part of a bed.
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“This is a sign that people continued to grow crops and live here even after the eruption, producing on top of the layer of ash and stone that covered and destroyed the entire city,” Pompeii director Massimo Osanna told Italian news agency Ansa.
Culture minister Dario Franceschini said the discoveries were “exceptional”.
Authorities in Pompeii, one of Italy’s most popular tourist attractions, have long battled to protect the site’s treasures from professional criminal gangs, light-fingered tourists, and the wear and tear of more than two million visitors each year.
Last week a French couple were fined €200 (£175) after police caught them a bag of Roman artefacts. They told officers they had stolen the 13 fragments of terracotta from a villa in the city as they “wanted to take home a souvenir”.