The sides drew 2-2 on Boxing Day but Glenavon have been punished for fielding a suspended player, David Elebert, in the match at Shamrock Park.
Under Irish FA rules, the match has now been recorded as a 3-0 win for the Ports with Glenavon also fined £350.
It means Portadown are now nine points behind one-from-bottom Carrick Rangers.
The case will provide a lift for embattled Portadown who were themselves similarly punished for playing a suspended player earlier in the season.
On top of that, they started the season on -12 points after being found guilty of paying a player whom they had registered as an amateur.
Glenavon got into trouble for including defender Elebert in their starting line-up for the traditional 26 December derby fixture.
Elebert had been suspended for one game from 19 December for five bookings, three of which were picked up during reserve team matches.
Glenavon felt Elebert had completed the suspension when he sat out a reserve fixture - but IFA rules dictate that such suspensions apply to the "more senior team".
The Lurgan club said they had checked Elebert's eligibility with the governing body before including him in their team.
They have four days in which to appeal against the Irish FA's decision.
The Premiership's bottom club Portadown have been handed a two-point boost following a disciplinary case against their Mid-Ulster rivals Glenavon.