Neville, who was appointed in 2021, has been relieved of his duties with Miami bottom of the MLS Eastern Conference with five wins and ten defeats this term.
Inter Miami assistant head coach Jason Morales will assume the role on an interim basis.
"When we appointed Phil we knew he would give Inter Miami his all and I have watched him work incredibly hard and with real commitment towards the ambitions we set out for the club," Beckham said.
"He and his family embraced Miami and he has devoted himself to the drive to bring success to the city and to our fans.
""Phil has made a real contribution to the culture of our club with his qualities as a leader and knowledge as a coach.
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"Sometimes in this game we have to make the toughest decisions and sadly we feel the time is right to make a change. I want to personally thank Phil for his hard work, his passion for our club and for his integrity as a person."
"I would like to thank the Inter Miami CF ownership group for their trust and making me a part of this project; the players and staff for their impressive commitment, dedication and hard work; and the fans for their unwavering support for the club since day one," Neville said.
"I'm grateful to have played a part in the growth of this club and wish Inter Miami CF all the best in the future."
Neville was appointed in January 2021 after a three-year stint in charge of the England women's national team.
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The highlight of his two-and-a-half years at the American club saw them reach the MLS Cup play-offs in 2022.
The end of his time with the club saw him snap back at fans and journalists during press conferences.