The last-gasp draw means that Costa Rica, who reached the quarter-finals in 2014, join Mexico as the second representative from the North, Central American and Caribbean region (Concacaf).
Both goalkeepers remained spectators for much of an at-times feisty affair, before Honduras collected an unexpected breakthrough midway through the second half.
A powerful header from Eddie Hernandez put Honduras in front in the 66th minute in the World Cup qualifier in San Jose, in a clash pushed back a day due to Tropical Storm Nate.
That strike appeared it would be enough for victory in a disjointed contest, until Waston popped up for a dramatic 95th-minute equaliser.
But there was late drama as the home side levelled in the fifth minute of additional time, Kendall Waston rising highest to head in a Bryan Ruiz cross.
Honduras is still in the hunt for a top-four finish, now fifth with nine points, just behind on goal differential to the United States in fourth. Up to that point, the fans and the players were resigned to have to wait to Tuesday, in the game against Panama, to officially qualify.
The Socceroos will be trying to advance to the next stage of the playoffs when they play Syria in Sydney on Tuesday night.
The U.S. hosts Panama on Friday, trailing its visiting third-place opponent by one point and level on points with Honduras, but ahead on goal differential for the fourth spot. Both teams are fighting for a direct spot in the next World Cup and will be looking to obtain the three points from this game.
In addition, the US could qualify with a loss if Panama and Honduras both fail to win Tuesday.
The group at large could well hinge on goal difference.