There was drama in the late kickoff in Wellington as Island Bay United were within minutes of claiming the day's upset only to succumb to two comebacks from Wellington Olympic and eventually go out 5-4 in a penalty shootout.
Barry Lewis gave away a 30th minute penalty that allowed Alex Palezevic to open the scoring only to redeem himself with Olympic's first equaliser in the 90th minute.
James Wypych put the underdogs back in front two minutes in extra time but Olympic drew level again this time through a 99th minute James O'Connor penalty.
The goalkeepers shone in the penalty shootout with Olympic's James McPeake making two legitimate saves - and another which was retaken and missed - to book his team's progression.
A four-goal haul to Damien Foster, which included a first half hat-trick, led Roslyn Wakari to a 8-1 mauling over Northern in Dunedin, while in Christchurch Danny Boys netted a goal in each half as Cashmere Technical beat Ferrymead Bays 2-0 in the day's other South Island fixture.
Bay Olympic were too good for East Coast Bays in a heavyweight clash in Auckland, running away with a 5-1 win, while Onehunga Sports won 4-1 at Fencibles and Manurewa edged Three Kings United 2-1.
Six more third round ties take place today, including mouthwatering derbies between Glenfield Rovers and Birkenhead United in Auckland.
A rematch of the 2011 final sees Napier City Rovers host Wairarapa while 2012 finalists Lower Hutt City meet Waterside Karori.
Nelson College take on Canterbury's Waimak United, Ellerslie face three-time winners Waitakere City and Palmerston North Marist travel to Tawa.
A flooded Caledonian pitch in Dunedin meant the fixture between Caversham and Dunedin Technical had to be postponed for player safety.
Details of the rescheduled fixture will be announced on tomorrow and the fourth round draw will take place as planned.