Jacobs is the first man to win the title other than the big sprint Usain Bolt since 2004 when he crossed the finish line in 9.8 seconds.
There was pre-race drama after a blatant false start by Hughes that kept him out and had to watch the final from the sidelines.
Hughes was to be the first Briton to run in the men’s race olympique 100m final since Dwain Chambers and Darren Campbell at the Sydney Games in 2000.
Speaking after the event, he blamed the false start on a left calf cramp as he took his position in the starting blocks.
“With the cramp, I moved,” he told the BBC.
“I think if I had been in the final I would have walked away with a medal, there’s no doubt about it.
“It was out of my control. It hurts. “
Hughes later said his cramp was “so severe” that he “just couldn’t stay” in his blocks despite having gone well during the warm-up.
The 26-year-old, who was born and raised in the British Overseas Territory of Anguilla, said he was trying to ‘think of something positive’ and refocus for the men’s event. 4x100m.
“I’m really heartbroken right now,” added Hughes.
“Wrong time and wrong place. “
The scenes recalled Linford Christie’s disqualification before the Olympic 100m final in Atlanta in 1996 following his two false starts.
The rules changed in 2010, so now a false start means instant disqualification.
Italian Jacobs, who only sprinted to the long jump in 2018, won the race in 9.8 seconds, edging American Fred Kerley by 0.04 seconds.
Canada’s Andre De Grasse won a second consecutive bronze medal in this event, having also finished third at Rio 2016.
Jacobs – who was born in Texas but moved to Europe with his Italian mother as a child – said after the race that winning the Olympic 100m title had been his dream since he was younger.
“It takes me about a week to figure out what happened,” he said.
“I won an Olympic gold medal after Usain Bolt, it’s amazing.
“Tonight, looking at the ceiling, I might realize. “
American Trayvon Bromell had been favorite to win the 100m title before the Games after setting the world’s fastest time this year at 9.77, but he failed to advance to the final.