The Seattle Sounders forward opened the scoring in the first half and then rendered Dexter Blackstock's equaliser in vain when he met Alan Gordon's cross in the 90th minute.
The US must finish in the top two of their CONCACAF group but this result means victory over Guatemala on Tuesday will seal their place in the final stage of qualifying for the 2014 World Cup in Brazil.
Johnson - axed in 2010 by then-boss Bill Bradley - was a surprise inclusion at the expense of Jozy Altidore but current coach Jurgen Klinsmann was soon vindicated, Graham Zusi's cross nodded in by the former Fulham man.
Blackstock tempered American celebrations just five minutes later when Peter Byers beat his man for pace and crossed low to afford the Nottingham Forest frontman a simple finish.
But Johnson had the final say, his aerial prowess again the difference, to keep World Cup destiny in his team-mates' hands.
Guatemala kept pace with Klinsmann's men on 10 points after staging a late raid of their own, Carlos Ruiz scoring five minutes from time to sink Jamaica 2-1.
Over in Group B, Jose Cubero's lone goal in El Salvador kept Costa Rica on course to join already-qualified Mexico in Brazil.
But there was no let up from the Mexicans, who kept up their perfect group record with a 5-0 hammering of eliminated Guyana, Manchester United striker Javier Hernandez among the goals with a 25-yard strike.
In Group C, Canada moved level with Panama on 10 points after a 3-0 win over an under-strength Cuba. Honduras remain in the mix, two points back, after a goalless draw with the Panamanians, with their final-round date with Canada on 16 October sure to be decisive.