El Bakkali clocked a time of eight minutes 6.05 seconds as American Kenneth Rooks took silver in 8:06.41 and Kenya's Abraham Kibiwot claimed bronze.
The win was overshadowed by the injury to Girma who tripped over a barrier on the last lap and fell hard to the track, lying motionless as medical staff rushed to attend to him.
His eyes were open and he was wearing a neck brace as staff members carried him off on a stretcher and a medic told Reuters that he was taken to a hospital.
French media reported he was conscious and speaking.
"Following his fall in the 3000m steeplechase, Lamecha Girma received immediate care from the on-site medical teams. Our thoughts are with him and we are sending him our very best wishes for a swift recovery," Paris 2024 said in a statement.
"Paris 2024 is in close contact with the Ethiopian NOC to stay updated on his condition."
The race had all the makings of an epic duel as El Bakkali waited in the middle of the pack before making his move with about 300 metres to go, chasing down Girma who was flying through the field.
Events took a jarring turn, however, when Girma fell, drawing gasps from the crowd.
El Bakkali chased down Rooks over the final bend but the American dug deep to produce a personal best time and claim a surprise silver.
The Moroccan held his arms out wide as he crossed the finish to become the first back-to-back winner of the event since Finland's Volmari Iso-Hollo in 1932 and 1936, while medical staff were still tending to Girma.
The fans at the Stade de France offered a smattering of applause as he was strapped to a stretcher and carried out through a tunnel.
"I actually didn’t know how bad the fall was - I didn’t know who fell until after the race - so I’ll just keep him in my prayers," said Rooks.
