The Clarets striker was fouled for the supposed spot-kick after 20 minutes, placed the ball down and prepared his run-up but three steps in he was halted.
Referee Simon Hooper had made the dreaded VAR signal and the set-piece was swiftly cancelled.
Vydra was judged to have been offside before the foul by Lee Mason, watching on screen at the VAR HQ in Uxbridge, some 235 miles away.
VAR fan Sean Dyche was fuming in his technical area as the flag was raised and Hopper kyboshed the free hit.
The visit of Barnsley in the FA Cup was one of nine ties chosen by the FA to feature a Video Assistant Referee and Dyche welcomed it’s apparently overdue arrival on his Turf Moor patch.
The gravel-voiced boss said: “I am a big fan of the system in theory.
“It’s about how it’s delivered and making sure it’s used in the best way to get the right outcomes and then I'm all for it.”
The club’s official account even employed some gallows humour around the incident but later apologised for any offence they might have caused.
During the half-time break, the club wrote: “HALF TIME: Burnley 0 Barnsley 0 VAR 1”
But when a string of uptight followers complained about the quick-witted musing, they decided to apologise.
They posted: “For clarification, we're not being critical of VAR with our half time post.
“It was meant as a light-hearted comment at a correct decision being made.
“We are fully in support of its use.”
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