Ecuador's Carapaz took the yellow jersey from overnight leader Tadej Pogacar of Slovenia. The pair are level on time. Remco Evenepoel and Jonas Vingegaard are third and fourth.
Intermarche rider Girmay, 24, who gave the Belgian team its first success on the Tour, is the third African to win on the Grande Boucle after South Africans Daryl Impey and Rob Hunter.
Multiple-tour winner Chris Froome was born in Kenya but competed for Britain.
Girmay won ahead of Colombian Fernando Gaviria and Belgian Arnaud De Lie in a chaotic finale marked by a late fall as the riders hit speeds of around 65 kph in the dash to the line.
The crash, in which the big favorite for the sprint, Jasper Philipsen, was involved, created a break in the peloton.
Two-time race winner Pogacar, gunning for a historic Giro-Tour double, did not fall but was delayed.
After two sweltering stages, the skies were shrouded in gray as they entered the northern Italian industrial city.
Girmay is more than just a sprinter, and was aided in his victory by the absence of stage favorite Philipsen.
He signaled his coming of age in 2022 when he became the first African to win a one-day classic at Gent-Wevelgem, aged 21.
It was his second Grand Tour stage win after the Giro d'Italia in 2022, where he injured an eye-opening a bottle of Prosecco on the podium.