The seventh-ranked Argentine lost just one set - the second set of the final - in five matches on the Royal Tennis Hall's hardcourts.
"It was great,'' said Nalbandian. "The conditions are perfect to play indoors. It could be faster or slower. I adapt my game to play here and I really like it.''
This was his second win of the season and his ninth career victory.
It was also the first singles victory by an Argentine in the 40-year history of the tournament.
Nalbandian won his first title of the year in Buenos Aires in February and lost the championship match in Acapulco the following week.
Both players held their serve in the third set until the seventh game, when Nalbandian broke to take a 4-3 lead on his fourth break point after the Swede netted a backhand.
Nalbandian then held to love to lead 5-3 and wrapped up the match with another break after the fourth-seeded Soderling double-faulted on match point.
"I was supposed to win in the second set when I was a break up, but he started playing better under the pressure,'' Nalbandian said.
"The third set was very tight. When I got the break I think I had everything under control.''
Soderling also lost the 2003 Stockholm final to Mardy Fish.
Nalbandian, who improved his head-to-head record against Soderling to 5-1, will next head to Spain to begin his defense of his Madrid Masters title.
"Madrid's altitude is 4-500 meters I think and it will take a few days to adapt,'' he said. "Of course it will be different, but I think I'm playing well now and I'll try to win again. But my big goal is the Davis Cup final.''
Argentina hosts Spain indoors in Mar del Plata on Nov. 21-23 in the Davis Cup final.
Roger Federer withdrew from the Stockholm Open, leaving Nalbandian as the top-seeded player.
Defending champion Ivo Karlovic also skipped the event.
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