The subject of the warrant is dead, the FBI said in a statement.
At an afternoon media briefing, Special Agent in Charge George Piro said the suspect opened fire.
Two agents with multiple gunshot wounds were taken to the hospital and are in stable condition, officials said. The third injured agent was treated at the scene.
FBI Director Christopher Wray identified the deceased agents as Special Agent Daniel Alfin and Special Agent Laura Schwartzenberger.
“Every day, FBI Special Agents put themselves in harm’s way to keep the American people safe. Special Agent Alfin and Special Agent Schwartzenberger exemplified heroism today in defense of their country,” he said in a statement. “The FBI will always honor their ultimate sacrifice and will be forever grateful for their bravery.”
The shootout, one of the deadliest in FBI history, brought a major law enforcement response to the area.
The FBI said its Inspection Division is investigating the shooting.
“The review process is thorough and objective and is conducted as expeditiously as possible under the circumstances,” the FBI statement said.
Alfin, 36, had worked cases of crimes against children for more than six years; Schwartzenberger, who was 43, for more than seven years.
Schwartzenberger had been an agent since 2005 and moved to the Miami bureau 11 years ago. She is survived by her husband and two children.
Alfin joined the FBI in 2009 and came to the Miami office in 2017. He was married with one child.
“They were valuable members of the FBI and will forever be heroes,” Piro said. “Our chosen profession is fraught with danger. Today this grim reality has taken two of our best from our family.”
The name of the suspect will not be released until the next of kin are notified, Piro added.
President Joe Biden expressed his condolences to the families of the victims on Tuesday.
“My heart aches for the families,” he said. “They put their lives on the line and it’s a hell of a price to pay.”
Last FBI agent fatally shot was in 2008
The FBI Agents Association (FBIAA) offered condolences to those injured and said the search warrant was in connection with suspected possession of child pornography.
“These Agents were working to protect the most vulnerable in our society. FBIAA stands with the Agents’ families and pledges our support to them during this difficult time,” FBIAA President Brian O’Hare said in a statement.
CNN’s Shawn Nottingham, Evan Perez, Jessica Schneider and Whitney Wild contributed to this report.