Frenchman Magnier pipped Tobias Lund Andresen in a frantic finish following 147 kilometres of largely flat racing from Nessebar to Burgas, in the first of the three early stages away from Italy.
He was one of a handful of riders who were ahead of a crash 600 metres from the line, which left the rest of the field to roll home in the knowledge that they would not lose any time due to the proximity of the accident to the finish.
Magnier, 22, claimed his first-ever Grand Tour win and also became the first Frenchman to wear the pink jersey for the overall lead since Bruno Armirail three years ago.
"I'm so proud of the team, and I'm so happy to be starting the Giro in such good form," said Magnier.
"The finale was chaotic after an easy day for everyone, on a narrow road. Beating such good sprinters here makes me very happy."
Magnier, who was born in Texas and moved to France as a toddler, is one of his country's young guns alongside Paul Seixas and last year clocked up 19 wins, the second-highest behind Tadej Pogacar.
His win on Friday is a return to form following a disappointing spring classics season, after beginning the year with two stages at the Volta ao Algarve.
Jonathan Milan, who won the sprinters' jersey at last year's Giro, could only finish fourth after escaping a crash which kept other sprinters like Dylan Groenewegen and Kaden Groves from contesting the stage finale.
Jonas Vingegaard, who rode with one fingernail painted red in support of a children's welfare charity, was one of those in the main pack held up by the crash.
Dane Vingegaard is the favourite for overall victory and on Saturday will be in the peloton for a hilly 221km ride from Burgas to Veliko Tarnovo.