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They took the lead in first-half stoppage time when winger Jon-Paul McGovern slid in from close range.
But Hartlepool hit back moments after half-time when substitute Efion Williams volleyed home.
After 71 minutes Pools struck again when fellow sub Jon Daly headed home Gavin Strachan's corner.
Wednesday manager Paul Sturrock took a gamble and brought on three substitutes.
The ploy worked as Pools defender Chris Westwood was sent off for bringing down newcomer Andrew Talbot, and fellow sub MacLean smashed home the late penalty.
Glen Whelan scored just three minutes after the restart, and teenager Talbot sealed the 4-2 win in stoppage time.
Hartlepool caretaker boss Martin Scott reckons that merely reaching the final in Cardiff bodes will for the club's future.
He said: "It just wasn't our day. Things went against us as three players came off injured and we had a player sent off.
"Sometimes it goes like that, but I cannot fault the players for how they have worked for me.
"I'm disappointed, but you have to look at the bigger picture. This club is going forward. It's one step at a time, but we are a force to be reckoned with now.
"If we can keep these players together we will be a good team next season."
The 24 teams competing in League One next season are:
Gillingham, Nottingham Forest, Rotherham (relegated from Championship)
Tranmere, Brentford, Hartlepool, Bristol City, Bournemouth, Huddersfield, Doncaster, Bradford, Swindon, Barnsley, Walsall, Colchester, Blackpool, Chesterfield, Port Vale, Oldham, and Franchise FC.
Yeovil, Scunthorpe, Swansea and Southend (promoted from League Two)