Forty drummers, trumpeters, clarinet and trombone players belted out the song.
The band marched in formations almost mimicking the famous choreographed zombie routine from the music video.
"It came out of nowhere," Philip Marfleet, 22, said who watched in awe with pals.
"We were stunned.
"They were practising some more traditional tunes and then all of a sudden they started playing Thriller.
"What a moment."
The lighting engineer, from Colchester, Essex, managed to capture it on his mobile phone.
He gathered with more than 20 foreign tourists outside The Guards Museum, in Birdcage Walk, central London to enjoy the spectacle.
He added: "It obviously wasn't the first time they had played it.
"It was a polished performance.
"A few foreign tourists asked me what it was all about, but I was unable to give them an explanation.
"I was as stunned as they were.
"At one point the musicians even appeared to be putting together some moves to go with the music.
"Instead of marching in straight lines they formed a triangle."
The oldest and best known band in the Army, based at the capital's Wellington Barracks, have actually been doing the routine for the last two months.
A MoD spokesman said: "The piece has been part of their summer repertoire for a number of events and they've been playing it publicly for the last eight weeks, including at the Windsor Tattoo.
"It is just a coincidence and not a tribute to Jackson."
It comes just a week after the world-famous regimental band signed a £1million recording contract with Universal Music.
Rapper Eminem and wacky pop star Lady Gaga are also signed to the label.
Onlooker Philip Marfleet, 22, of Colchester, Essex, filmed them on his mobile.
He said: "The band were practising traditional tunes in Birdcage Walk then suddenly started playing Thriller. At one point they even appeared to be putting together some moves to go with the music."
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