Defender Rocky Bushiri played the full 90 minutes of the 1-1 draw, which the Championship side won 3-1 on penalties, despite being banned after picking up two bookings in previous group fixtures, the 1-0 defeat to Falkirk and 4-1 victory over Bonnyrigg Rose.
The SPFL charged the Easter Road side with breaching competition rules – which state an immediate one-match suspension applies to players accumulating two cautions before the second round of the Cup.
The club were summoned to a disciplinary hearing on Thursday where SPFL bosses confirmed that Morton had been awarded a 3-0 win, with Hibs receiving a £5000 fine, £4000 of which is suspended until June 30, 2023 pending any further breaches.
The Leith side were also reprimanded and warned over their future conduct.
The punishment means Hibs finish on six points in Group D and can no longer qualify for the knock-out stages of the competition having already been on the verge of an embarrassing early elimination following two defeats to lower league opposition.
A club statement read: “Hibernian FC can confirm that the Club has been penalised by the SPFL for breaching rules and regulations in the Premier Sports Cup.
“During the final group stage match against Greenock Morton, the Club featured a player who was subject to a one-match suspension in the competition.
“Following an SPFL hearing on Thursday 21 July 2022, it has been confirmed that last night’s game has been recorded as a 3-0 win to the cinch Championship side.
“Hibernian FC would like to apologise to its supporters, to Greenock Morton, and to the SPFL for the rule breach.
“The administrative error has been investigated internally, and whilst processes are already in place to prevent issues of this nature from occurring, additional steps have been added to ensure this doesn’t happen again.”
Stranraer were also cited for fielding an ineligible player in Paul Woods during their Premier Sports Cup match with Forfar Athletic. The League Two side also received a 3-0 defeat and a £1,000 fine with £500 of it suspended.
It now means three clubs have suffered punishments for similar offences in this season’s tournament after Elgin City were charged for playing defender Daryl McHardy in their match with Ayr United.