It was a sweet moment for Holmes against his former club and means the in-form Cobblers are now within three points of the play-off places in League Two after their third straight victory.
Both sides created chances in an entertaining game and Chris Wilder conceded afterwards that Town 'were maybe a bit fortunate,' while praising his players for their defensive qualities as Pompey pressed for an equaliser.
Northampton now prepare the long trip to Plymouth Argyle on Saturday knowing that their hopes of making the play-offs are alive and kicking.
Portsmouth manager Andy Awford was left to rue a defensive lapse from his side, saying: ‘We switched off from a throw-in. We had the ball attacking up our left-hand side, they clear it, it goes out for a throw-in and we haven’t reacted quickly enough.'