The plane was heading to Luton when it blew two tyres shortly on take-off from Teterboro airport in New Jersey.
The jet was diverted to New York Stewart International Airport but the pilot was forced to circle for several hours to burn off fuel.
Several fire and ambulance crews were at the site as the plane landed safely shortly before 4pm (9pm UK time).
Afterwards, Malone wrote on Twitter: “I landed guys. Thank you for your prayers.
“Can’t believe how many people wished death on me on this website. F*** you. But not today.”
Photos posted on Instagram by his entourage ahead of take-off showed Malone boarding the Gulfstream IV jet.
The Federal Aviation Administration said the plane had 16 people on board.
Malone performed at MTV’s video music awards in New York on Monday night and took home the song of the year award for his hit Rockstar.
The 23-year-old is due to appear at Reading and Leeds music festival this weekend.
After reports emerged that Malone was on board the troubled flight, fans of the rapper began gathering at the landing site.
“We came down because he had the biggest day of his life yesterday and we wanted to make sure he is safe,” Jessica Kielb said.
Malone has achieved four UK top 10 hits including a UK number one last year with Rockstar featuring 21 Savage.