The orbiter's navigation system, which works by tracking the position of stars, likely became confused after mistaking dust particles near the comet surface for faraway heavenly bodies, the European Space Agency (ESA) said.
"We lost contact with the spacecraft on Saturday evening for nearly 24 hours," mission manager Patrick Martin said on ESA's Rosetta blog.
"Preliminary analysis by our flight dynamics team suggests that the star trackers locked onto a false star," he said, as it approached within five kilometres (3.1 miles) of the frozen space rock blasting out jets of icy dust.
The spacecraft, perhaps best known as the mothership of surface probe Philae, entered "safe mode", switching off its science instruments and severing contact with Earth.
Ground controllers had to send "blind" commands to the orbiter, without knowing at first whether they were received or executed, to unblock the star trackers.
"It was an extremely dramatic weekend," said spacecraft operations manager Sylvain Lodiot.
Contact was reestablished by Monday, but Rosetta's position along its orbit of the comet remained unknown for several more hours, until ground controllers could analyse the first navigation images sent back home.
"I confirm the spacecraft status is back to normal mode, with instruments back in science operations," Martin told AFP on Thursday.
Exploring time capsules
The spacecraft's location was pinpointed, and flight manoeuvres performed on Tuesday night to move it further away from the comet, into a 30 km orbit.
Rosetta, with Philae riding piggyback, arrived at comet 67P/Churyumov-Gerasimenko in August 2014 after a ten-year, 6.5-billion kilometre journey from Earth.
In November that year, it sent down Philae, a 100-kilogramme (220-pound) lab equipped with 10 instruments for sniffing and prodding 67P.
After bouncing several times, Philae ended in a ditch, shadowed from the Sun's battery-replenishing rays. But it managed to run about 60 hours of experiments and send home reams of valuable data before running out of energy and entering standby mode.
As 67P neared the Sun on its elongated orbit, with Rosetta in tow, Philae emerged from hibernation in June 2015 and send a two-minute message to Earth via its mothership.
The lander entered silent mode in July 2015 after eight intermittent communications with Earth, and in February this year, ground controllers said they had given up trying to contact the tiny robot lab.
This was not Rosetta's first star-tracking mishap in April 2015 it similarly lost its way and entered safe mode after running into blasts of comet dust and gas.
The EUR 1.3-billion ($1.45-billion) mission was conceived to unveil the secrets of comets, believed to be time capsules from the birth of the Solar System.