The Northern Irishman was seeking redemption in the Swiss mountains after bogeying the last and losing a play-off 11 years ago in his rookie season, but it was to be more heartbreak for the world number two.
He admitted after bogeying three of his last five holes in round three that he felt "flat" following his FedEx Cup win in Atlanta seven days ago, and his race looked to be run after 10 holes of round four as he slipped four shots off the lead.
He made four birdies in a row from the 12th to put himself back into contention but that could not keep pace with playing partner Soderberg, as the Swede made five straight from the 10th.
Another McIlroy gain on the 17th moved him to 14 under and, when Soderberg three-putted the same hole for a double-bogey, they went up the last all square.
McIlroy sent his tee shot into the trees on the right but made a fantastic up-and-down from distance and a missed birdie putt from Soderberg meant the pair were going to extra holes alongside Lorenzo Gagli, Andres Romero and Kalle Samooja.
Gagli found water with his second on the trip back up the last, while Romero missed the green, leaving McIlroy, Soderberg and Samooja with birdie putts after a trio of excellent approaches.
Soderberg holed from ten feet to put the pressure on his rivals and he was crowned the champion as McIlroy and Samooja both missed their opportunities.
"Too many mistakes," McIlroy told Sky Sports Golf. "I think I made 13 bogeys during the week. I made enough birdies but I just didn't have it over the weekend.
"It's been another solid week, coming back across the Atlantic. Now I'm looking forward to a couple of weeks off."
Spaniard Adri Arnaus and Frenchman Mike Lorenzo-Vera finished a shot outside of the play-offs, one clear of a group containing England's Tommy Fleetwood.