Northumbria Police said a 41-year-old man from North Shields has been charged with a public order offence after allegedly making the comments following Newcastle's 1-0 Carabao Cup win over Manchester City on Wednesday.
He is due to appear at Newcastle Magistrates' Court on October 18 but until then he has been given bail with conditions. The accused has also been banned from St. James' Park during Newcastle's matchdays.
Superintendent Rob Bosson of Northumbria Police said: "First and foremost, I would like to stress that this type of behaviour has absolutely no place in our communities – and we take reports of this nature very seriously.
"As soon as we were made aware of the video, an investigation was immediately launched, with officers working hard to identify a suspect who has since been arrested and charged.
"I would like to thank both the public and our partners for their continued support. We would ask people not to speculate either in the community or on social media. Doing so could potentially jeopardise live criminal proceedings."
Seven Manchester United footballers were among 21 people killed in the plane crash in 1958 when the 'Busby Babes' were flying out of West Germany after a European Cup game in Belgrade.
A Newcastle United spokesperson added: "Tragedy-related chanting and gesturing is completely unacceptable and Newcastle United is committed to working with authorities and the wider football community to eradicate it."