Eulalio now leads race favourite Jonas Vingegaard by just 27 seconds, an advantage that had been over six minutes when the Portuguese rider took control after last week's rain-lashed stage five.
Eulalio had led by over two minutes overnight but looked set to lose the pink jersey on Tuesday before rallying in the latter half of the long time trial.
"I suffered, suffered and suffered," said Bahrain Victorious climber Eulalio. "But here I am still in the lead."
Ineos rider Thymen Arensman had a great day and climbed to third at one minute and 57 seconds, while Felix Gall dropped to fourth at two minutes and 24 seconds. Australian Ben O'Connor climbed to fifth at two minutes and 48 seconds.
The potentially decisive stage was held on a flat 42km coastal run between Viareggio and Massa on the Tuscan coast.
This was an eighth Giro stage win for Ganna, seven in the time trial, and the one-minute 52-second winning margin speaks for itself.
"This was built for me," said the former track specialist who like Tuesday's runner-up Arensman rides for Ineos. "This is the result of the work the team did this winter."
A picture-postcard run, the same route which often features on the Giro warm-up race, the Tirreno-Adriatico, included two long, straight stretches, meaning power rather than technique was the order of the day.
While Ganna's win was expected, so was the shake-up in the overall standings with Jai Hindley and Gall losing time.
Wednesday's stage 11 is a hilly affair with Eulalio tipped to keep the overall lead as far as the weekend mountain stages.