Olympic champion Jacobs defeated in European Indoor Championships
Jacobs, who appeared to have suffered an injury in winning his semi-final in Istanbul, was slower out of his blocks in the final than the fast-starting Ceccarelli who won in 6.48sec to Jacobs' 6.50 for second.
Henrik Larsson of Sweden took the bronze medal in 6.53 while one of the pre-race favourites, British sprinter Reece Prescod, made a disastrous start and finished last.
Ceccarelli, 23, an indoor specialist who does not feature among Europe's best in the 100m outdoors, showed that his victory over Jacobs in the Italian indoor championships had been no fluke.
The new European champion, whose grandfather Gastone Giacinti was a goalkeeper for then-Serie A club Foggia in the 1970s, said he had been as shocked as anyone by his sudden breakthrough this winter.
"It was absolutely mental. I didn't expect that. It's been three years that I didn't have the possibility to run a complete season because of injuries," he said.
"I didn't know what to expect from this indoor season, (so) I'm very happy for what happened in the space of 50 days."
Jacobs, whose outdoor season last year was hampered by injuries, confirmed he had been nursing a hamstring problem.
"This is not the medal that I wanted, I obviously wanted the gold," he said. "My leg wasn't the best today, it was really tough today. My teammate did great.
"Now is the end of the indoor season so my focus is on the outdoor. I will try to recover from the hamstring injury as soon as possible and get back to the track."
Bol eases to gold
In the women's 400m, there was a far smoother ride for world record holder Femke Bol who pulled away as she entered the second lap and strode clear to win in 49.85.
The Dutch athlete's time was more than half a second slower than the sensational world record of 49.26 she set in February but it was easily enough for her to beat her compatriot and training partner Lieke Klaver and retain the title she won in 2021.
Bol's performances this winter, and increased speed over the flat, have whetted the appetite for her clashes to come this summer with American world and Olympic champion Sydney McLaughlin-Levrone in the 400m hurdles.
Karsten Warholm, the Olympic champion and world record holder in the men's 400m hurdles, won the men's 400m title despite tying up badly at the end and nearly being caught on the line by Julien Watrin of Belgium.
Warholm was timed at 45.35 and Watrin was rewarded with a national record of 45.44 for pushing the Norwegian into a dip finish which left him sprawled on the track.
In the women's 1500m, Britain's Laura Muir broke away at the bell for the final lap and was a class above the field, finishing in 4min 03.40sec to take the title at these championships for the third time. Claudia Mihaela Bobocea of Romania won the silver.
With three 1500m titles and two gold medals at 3,000m, Muir moves ahead of sprinters Colin Jackson and Jason Gardener as the British athlete with the most European indoor titles.
Her British teammate Keely Hodgkinson eased into Sunday's women's 800m final where she will be bidding to retain her title.
There was another emotional gold medal for home nation Turkey, still mourning the tens of thousands dead in a devastating earthquake in the south of the country, when Tugba Danismaz won the women's triple jump.
Her jump of 14.31m pipped Dariya Derkach of Italy who reached out to 14.20m.