The American led from start to finish to easily win the race five metres ahead of Austrian Markus Rogan only to learn he had been disqualified for an illegal turn on the last lap.
Rogan was promoted to first place but the U.S. team filed a protest against the decision and the disqualification was overturned.
"I don't know what I did," Peirsol told reporters before the appeal was heard. "Nobody told me anything, it sounds bogus to me."
Peirsol had won gold in the 100 backstroke on Monday and was a hot favourite to complete the double by winning the 200.
He had the race under control from the outset, opening up a big lead over the field from the first lap and pulling away to reach the finish first in one minute 54.95 seconds.
Austria's Markus Rogan came home second in 1:57.35, just ahead of Romania's Razvan Florea in third, who touched in 1:57.56. Britain's James Goddard was fourth in 1:57.76.
"I don't want to pass judgement because Aaron is one of my best friends," Rogan said.
"No medal is as beautiful as a friendship."