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Phelps continued to struggle to meet expectations in the old-style suit that will be required as the only eligible next year.
Phelps, who won a record eight gold medals at the 2008 Beijing Olympics, clocked 1 minute 53.93 seconds, more than two seconds behind Townsendin, who won in 1:51.79.
Earlier, Phelps failed to qualify for the 100m butterfly final after ending 11th in qualifying heats in 51.06 seconds. Kaio Almeida of Brazil was fastest in 50.34.
It was the third final that Phelps missed at the event. On Tuesday he failed to qualify for the finals of the 100 freestyle and 100 backstroke, in which he was disqualified for swimming too long under water.