In the fifth minute of stoppage time, Bryan Ruiz crossed to Waston, and the Vancouver Whitecaps defender outjumped Maynor Figueroa and Johnny Palacios to head the ball past Donis Escober from eight meters out.
Costa Rica join Mexico in qualifying for the World Cup in Russian Federation and US will fill the third CONCACAF space if they can beat Trinidad and Tobago in their next match.
Costa Rica's Kendall Waston (C) heads to score against Honduras during their 2018 World Cup qualifier football match, in San Jose on October 7, 2017.
CONCACAF's six-nation final round of qualifying concludes on Tuesday, when the United States travels to Trinidad and Tobago, Honduras hosts Mexico and Panama hosts Costa Rica.
The United States have 12 points and are favourites to take the third automatic spot but Panama and Honduras, both on 10, are still in with a chance.
When it comes to separating the two sides locked on ten points, if Panama match Honduras' result only a five-goal swing in goal difference in favour of Los Catrachos can prevent Panama coming out on top.
Meanwhile, Nigeria became the first team from Africa to qualify, doing it with a game to spare and emerging from the so-called "group of death" after beating Zambia 1-0 at home on Saturday.
The group also contained African champion Cameroon and the former top-ranked African team, Algeria, who had both already been eliminated. The anguish of Honduran fans having their first World Cup since 2010 slip from the jaws of victory was almost as compelling as video of the goal.
In addition, the USA could qualify with a loss if Panama and Honduras both fail to win on Tuesday.