Armando Dobra netted a brilliant strike in extra-time but Chesterfield’s former Town players and staff were ultimately defeated 4-3 on penalties by Notts County following a 2-2 draw in the Vanarama National League play-off final at Wembley.
The Spireites took the lead from the penalty spot in the fifth minute via Andrew Dallas and were the better side throughout but conceded three minutes from time when a John Bostock free-kick squirmed past keeper Ross Fitzsimons.
Dobra brilliantly restored the lead three minutes into the additional half an hour, but the Magpies hit back through Ruben Rodrigues in the 108th minute and won the shoot-out, which Cook was unable to watch, the ex-Blues boss disappearing down the tunnel.
In addition to Dobra, the Spireites are managed by former Blues boss Paul Cook, who took charge in February 2022 and this season led Chesterfield to third in the National League having taken them to the 2013/14 League Two title in his previous spell in charge.
Former Blues winger and coach Gary Roberts followed Cook to the Derbyshire club as a first-team coach and last summer they signed Dobra after his contract at Town was settled and full-back Bailey Clements, who had been released from Portman Road, with the pair both in the starting XI at Wembley.
Dyer, who became close to Cook during their time at Portman Road together, joined the off-field staff as a first-team coach earlier this year.
The Spireites, who finished 23 points behind the second-placed Magpies, beat 10-man Bromley 3-2 after extra-time in their play-off semi-final.