Germany meanwhile overcame Costa Rica by the same margin 2-1.
In a match postponed a day because of a tropical storm, Eddie Hernandez's header from Romell Quioto's cross put Honduras ahead in the 66th minute.
Costa Rica join Mexico in qualifying for the World Cup in Russian Federation and United States of America will fill the third CONCACAF space if they can beat Trinidad and Tobago in their next match.
Waston has three global goals, including a header off a Christian Bolanos' 68th-minute corner kick on March 28 that gave Costa Rica a 1-1 draw at Honduras.
The Waston goal means the United States likely needs at most a draw at Trinidad and Tobago on Tuesday (Oct. 10) night to qualify for its eighth straight World Cup show.
Costa Rica had a golden chance to take the lead in the 60th minute.
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Costa Rica (16 points) will finish second to Mexico (21), with those as the only two CONCACAF sides to have booked their tickets to Russian Federation.
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.
The US have 12 points following their 4-0 win Friday over Panama and would qualify with a win or draw in Trinidad on the final night of the qualifiers.
The United States now occupies third place in the table after beating Panama 4-0 on Friday night, which leaves Bruce Arena's side in control of its own destiny heading into the final match of the Hexagonal.
In addition, the USA could qualify with a loss if Panama and Honduras both fail to win Tuesday. They were quarter-finalists in Brazil in 2014 and reached the knockout stage in Italy in 1990.