Despite Pompey being firmly opposed, third-tier clubs voted in favour of a £2.5m wage ceiling being implemented at the start of the 2020-21 season.
A cap of £1.5m in League Two was also brought in.
Backed by the Blues, the Professional Footballers’ Association (PFA) immediately challenged the caps, saying they were ‘unlawful and unenforceable’.
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PFA chief executive Gordon Taylor welcomed the news in a statement after a decision was made.
However, Holt was a strong supporter of a salary cap being brought in after finances in the lower leagues were hit hard because of the coronavirus crisis.
And the Stanley chairman is clearly disappointed the wage ceiling has been axed.
Writing on Twitter, Holt said: ‘Been asked a few times for my take on Gordon’s ramming of the salary cap.
‘Football has been incapable of managing formulae like FFP (financial fair play) and SCMP (salary cost management protocol).
‘A landscape littered with broken clubs amply demonstrates this.
‘A salary cap that I thought even we at the @EFL couldn’t get wrong... well money has talked and we even managed to get that wrong.
‘The majority of clubs voted for something that couldn’t be sustained. Welcome to English football.
Sports lawyer Nick De Marco QC revealed that he played a major role in fighting the salary cap on the PFA's behalf.
He told of his delight that the union's appeal was upheld.
In response, Holt said: ‘When you’re finished preening yourself about your ability to beat @EFL in court… I want rules that would keep you lot a million miles away from our game.
‘It’s a toss up for me who’s worse for the game. You lot or administrators. You’re taking candy off a baby, pipe down.’