The resulting footage is part of a project using hi-tech scanning methods to explore animals' anatomy.
It took 132 hours for the snake to fully digest the rat, the scientists said. Their work has revealed other strange insights into python digestion.
They presented the study at the Society for Experimental Biology's annual meeting in Prague, Czech Republic.
The researchers carried out a computer tomography or CT scan of an anaesthetised 5kg Burmese python one hour after it had devoured the rat whole.
They also used a technique called magnetic resonance imaging (MRI) to study the creature's internal organs.
By using contrast agents, the scientists were able to highlight specific organs and make them appear in different colours.
A series of MRI images revealed the gradual disappearance of the rat's body. At the same time, the snake's intestine expanded, its gall bladder shrank and its heart increased in volume by 25%.
The researchers, Henrik Lauridsen and Kasper Hansen, both from Aarhus University in Denmark, explained that the increase in the size of the snake's heart was probably associated with the energy it needed to digest its meal.
"It's a sit and wait predator," explained Mr Lauridsen. "It fasts for months and then eats a really large meal.
"It can eat the equivalent of up to 50% of its own bodyweight, and in order to get the energy out of the meal, it has to restart the intestinal system very fast."
The researchers, who are both based at the university's Department of Zoophysiology and the MR Research Centre at Aarhus, say that their approach has several advantages over the "subjective and sometimes misleading" interpretations of dissections.
Dissection induces changes, explained Dr Hansen. "For example, after opening the dense bone of a turtle shell, the lungs will collapse due to the change in pressure.
"And to use these techniques you don't have to kill the animal," he added. "We can do this using live animals and revisit the results over and over again."
The images, they say, will be valuable tools in future studies of animal anatomy for both research and education.
As part of the project, they have produced similarly spectacular images of several other species, including frogs, alligators, turtles, swamp eels and bearded dragons.

The first attack targeted a police station in the eastern city of Van, killing one police officer and two civilians. Some 73 people were hurt.
Hours later, a police station in Elazig was hit, killing at least three police officers and wounding 146 people.
Turkish officials blamed the Kurdish militant group, the PKK.
The PKK has carried a series of bombings targeting the police in the largely Kurdish south-east since a ceasefire with the government broke down last year.
Television footage showed plumes of smoke rising above the destroyed police building in Elazig.
The force of the blast blew out nearby cars, uprooted trees and left a large crater outside the building.
At least eight people were killed in two attacks on police vehicles in nearby Diyarbakir and Kiziltepe last week.
Since last month's failed coup in Turkey, there has been much talk of national unity.
But this has not included the pro-Kurdish political party which the Turkish authorities say supports the PKK, reports the BBC's Turkey correspondent Mark Lowen. The pro-Kurdish HDP denies any link to the militants.
Scientists have used the latest imaging techniques to look inside a python that had just swallowed a rat whole.
[NEXT_CONCEPT]
Two big car bombs have hit police stations in separate cities in Turkey, killing six people and wounding at least 219 others.