After Lamont Marcell Jacobs won men's 100m, Dina Asher-Smith pulls up with a cramp
A three-time European gold medallist in 2018, Asher-Smith slowed after 60m because of cramps in both her calves.
Italy's Jacobs ran 9.95 seconds to beat British defending champion Zharnel Hughes (9.99) to the men's title.
Team-mate Jeremiah Azu ran a personal best 10.13 to take bronze.
Neita clocked 11.00 as Germany's Gina Luckenkemper (10.99) delivered a hugely popular home victory ahead of Switzerland's Mujinga Kambundji in a photo finish.
Earlier, Briton Jacob Fincham-Dukes thought he had clinched his first major championship medal with silver in the men's long jump at the Olympiastadion.
However, an appeal found the 25-year-old's season-best opening leap of 8.06m was a foul, and he was demoted to fifth based on his next-best jump of 7.97m
In two thrilling 100m races, Israel Olatunde - the first Irish athlete to reach the European 100m final - set a national record of 10.17 to place sixth ahead of Britain's Reece Prescod, who finished fourth in 2018.
In the women's event, Imani Lansiquot was fifth in 11.21, with Asher-Smith eventually jogging across the line.
Asher-Smith entered the championship bidding to defend the three titles she won in 2018 in the 100m, 200m and 4x100m relay.
The 26-year-old was forced to withdraw from the Commonwealth Games after pulling up with a hamstring strain while competing for Great Britain in the women's 4x100m relay final at the World Championships in July.
By then, she had equalled her British record to take an agonising fourth in the 100m in Eugene - missing out on a medal by just 0.02 seconds - before winning 200m bronze.
That success, after which she revealed she had been struggling away from the track following her grandmother's death, marked her return to a significant championship podium after a hamstring injury wrecked her Olympics campaign.
There was to be no repeat in Munich - though it appears the problem she suffered was not a serious one.
"I got cramp in my calves, and I can't be running on two cramping calves," Asher-Smith told BBC Sport.
"I'll chat about my recovery and how I'm hydrating. I feel good, which is why I'm frustrated.
"I wasn't about to go and run a whole race on two cramping calves and possibly tear them. Frustrated, it's just very annoying."
Meanwhile, team-mate Neita, who successfully added to her Commonwealth bronze, lost out in a tight finish and also said she had suffered cramps.
"I was cramping up a lot. I haven't cramped all year. I was praying on the start line that I got through in one piece," Neita said.
"I honestly wasn't going to race, but who will believe me if I said I was cramping up before? I got a medal somehow."
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