The Greens took the lead midway through the first half and had a man sent off 10 minutes later but were still able to hold out their A-League opponents to secure a famous victory at Kingston Heath on Tuesday night.

It is just the sixth time an A-League side has been beaten in the cup by a team outside of the national competition.

Rudan was coaching the Phoenix in his first competitive match and fielded a strong starting team featuring former Socceroos Nathan Burns and Mitch Nichols, Fijian star Roy Krishna and new recruit Steven Taylor, an ex-Premier League player for Newcastle United.

Yet there was little discernible difference between themselves and Victorian NPL powerhouse Bentleigh, who made the FFA Cup semi-finals in 2014.

Marco Jankovic, the son of former Real Madrid defender Milan Jankovic, put the Greens in front with a header from a corner kick in the 23rd minute.

Soon after, James Kelly was shown his second yellow card and sent off following a late challenge on another new Wellington signing Michal Kopczynski.

But the Phoenix did not have the quality in the final third to break down a resolute Bentleigh defence.

Meanwhile, Western Sydney dodged a potential disaster of their own, edging minnows Hellenic Athletic 4-3 at the death in Darwin.

Hellenic came from 2-0 down to twice draw level with the Wanderers and were centimetres away from taking the lead - only for Brendon Hamill to clear a Robert Kilmartin header off the line in the 81st minute.

Instead, Roly Bonevacia won it for the Wanderers with a goal from close range in added time to shatter any hopes of a miraculous upset from the locals.

Newcastle Jets had no such troubles at Cbus Super Stadium, beating a plucky Gold Coast Knights 1-0 courtesy of an early Nikolai Topor-Stanley goal to finally register their first FFA Cup win in the tournament's five-year history.

In the other matches involving A-League sides, a first-half Kosta Barbarouses goal saw Melbourne Victory defeat Perth Glory 1-0 in the west.

In Redcliffe, a stunning Bruno Fornaroli goal in the last minute of extra time gave Melbourne City a 1-0 victory over Brisbane Roar.

The match looked destined for a penalty shootout but Fornaroli's lash from outside the box was enough to book City's spot in the next round.

Play was stopped for more than half an hour in the first half following a suspected head or neck injury to City midfielder Luke Brattan, who was taken from the field in an ambulance.

Devonport Strikers are also into the round of 16 for the second time after upsetting Northcote City 3-1 in Melbourne, becoming the first Tasmanian team to win an FFA Cup match on the road.

Australian Associated Press