"It is definitely the nicest victory of the year," Jönsson said.
The reigning world bronze medallist, who had already won the discipline's crystal globe, finished ahead of Norwegian duo Petter Northug and Ola Vigen Hattestad for his 10th victory on the World Cup circuit.
Despite his second place, triple world champion Northug will be unable to dethrone Switzerland's Dario Cologna from atop the overall World Cup standings.
Jönsson's Sweden team mate Marcus Hellner was forced to pull out of the race with a sore throat.
The Royal Palace Sprint is a World Cup tournament which in 2011 was being held for the eighth time.
The race takes place in central Stockholm on a course stretching 1,030 metres around the Baroque style palace which dates back to the 13th century and is located on the edge of the Old Town.