Anything but a Panama victory would have seen both the Americans and Costa Ricans advance to next year's World Cup finals, and despite a late equaliser from Panamanian Roberto Chen in Tegucigalpa, the Hondurans held on for a point.
The draw did cost Honduras the chance of virtually sealing their own place at Brazil, while Panama kept theirs alive, as they remain three points behind third-placed Honduras.
The top three teams in the six-nation group qualify automatically, while fourth - Panama as it stands - go to the intercontinental play-off versus New Zealand.
Honduras paid the price for failing to hold onto a lead on two separate occasions on Tuesday, after Carlos Costly put them ahead on 28 minutes.
They lead by that goal at the interval, only for Gabriel Torres to equalise on 50 minutes for the visitors.
Wilson Palacios restored Honduras' lead 11 minutes later and they held that buffer into injury time.
But the hearty Panamanians rained on the parade, as Chen earned them a point in the second minute of additional time.
The result sealed a spot in Brazil for the USA, who earlier defeated Mexico 2-0.
Eddie Johnson and Landon Donovan were both on target in Columbus, as the Americans climbed top of the qualifying group over the Costa Ricans.
Mexico remain fifth on eight points, level - even on goal difference - with Panama in the race for the play-off spot.
Costa Rica were kept to a 1-1 draw away at Jamaica's Independence Park with the hosts earning just their fourth point in eight qualifying games.
The Costa Ricans were on target for victory but an injury-time equaliser from Jermaine Anderson gave the Caribbean nation something to savour.
