Hughes tapped in Yoann Arquin's pinpoint cross from the right after 81 minutes before Zoko nodded in Alan Sheehan's corner, which was badly fumbled by Pompey keeper Simon Eastwood, three minutes from time at Fratton Park.
Pompey - who have yet to secure a point in League One in 2013 - came agonisingly close to edging ahead after just two minutes when Jed Wallace's cross from the right wreaked havoc in the County penalty area.
Ashley Harris stabbed a shot towards goal, but Gary Liddle saved his side with a desperate clearance off the line.
County thought they had opened their account after 28 minutes, when Pompey defender Ricardo Rocha headed Jamal Campbell-Ryce's cross into his own net. But referee Gavin Ward ruled it out for a push.
Neither side looked capable of producing a telling touch in the final third, until the Magpies struck with a late double thanks to Hughes and Zoko.
County ended the game with 10 men after Neal Bishop was sent off following an off-the-ball altercation with Pompey skipper Johnny Ertl in the final minute.