Palm Beach Gardens police Officer Nouman Raja believed it was an abandoned car and stopped to investigate, according to authorities.
Raja was on duty but was wearing civilian clothing and driving an unmarked car, police Chief Stephen Stepp told reporters.
"As the officer exited his vehicle, he was suddenly confronted by an armed subject," Stepp said.
"As a result of the confrontation, the officer discharged his firearm, resulting in the death of Mr. Corey Jones."
The death of Jones, who is black, is the latest in a series of controversial police shootings that have sparked nationwide protests and questions on race and policing.
His death lit up social media, with people tweeting demands for justice using hashtags #Justice4Corey and #CoreyJones.
Source: Investigators believe confusion was at play
Authorities said they recovered a handgun at the scene and paperwork showed Jones bought it three days before the shooting.
Officials have not said whether that gun was fired. There is no dashboard camera footage of the shooting nor was the officer wearing a body camera.
What led to the confrontation and shooting is unclear.
Mathew Huntsberger, a friend and band mate of Jones, told CNN that they'd played together late Saturday night and early Sunday morning. Jones called Huntsberger later asking for help after his car broke down.
Huntsberger arrived, and they called a tow truck. He said that he left Jones less than an hour before the shooting.
"The tow truck was on the way. We didn't think anything was going to happen," said Huntsberger. "It was complete shock."
He described his friend as a peaceful guy.
"We just want to let everyone know that he didn't deserve this. And, that he was a good person -- a peaceful person," Huntsberger said.
A source close to the investigation told CNN on condition of anonymity Wednesday that investigators believe the shooting was a result of Jones and Raja misidentifying each other.
The source said Raja felt he had to check the car because there had been burglaries in the area recently and that burglars had parked near the ramp where Jones' vehicle was.
Raja "was working as part of a detail related to a string of burglaries in the city," Stepp told reporters Tuesday.
The anonymous source told CNN on Wednesday that investigators believe Raja may not have made it sufficiently clear he was an officer and that Jones may not have heard what the officer said.
Palm Beach Gardens police have not said how or whether Raja identified himself to Jones.
Search for answers
Friends of Jones were stunned and saddened.
"Just really sad for Corey's family. They lost an amazing person, a really special human being and my heart goes out to them more than anything," Boris Simeonov, who was in the same band as Jones, told WPTV.
Jones' family members said they will do whatever it takes to get answers.
"Corey Jones was a God-fearing man who dedicated his life to doing the right thing. He lived every moment to the fullest and was an inspiration to many; the kind of son, brother and friend people could only hope for," his family said.
"Rest assured, we are working diligently with our legal team to determine exactly why this plainclothes police officer in an unmarked car would approach Corey."
Jones' family attorney is Benjamin Crump, who represented the families of Trayvon Martin and Michael Brown.
Martin, an unarmed black teenager, was fatally shot by George Zimmerman, who was acquitted of murder charges in 2013. Brown was killed last year by an officer in Ferguson, Missouri.
Crump said the scene of Jones' shooting was "surrounded by businesses with surveillance video," and that a nearby streetlight also had a video camera. He called on police to gather and release any relevant footage.
"What we don't want to do is rely solely on the person who killed Corey Jones" for an account of the shooting, Crump told CNN's "New Day" on Wednesday.
The Palm Beach County Sheriff's Office is conducting an investigation, as is the office of State Attorney Dave Aronberg.
Raja, who has worked for the police department since April, is on paid administrative leave.
The department has no records of complaints, disciplinary actions or internal affairs investigations against him while there, Stepp said.
A rally is planned Thursday outside the Palm Beach Gardens Police Department.