History repeated itself for McIlroy at the Crans-sur-Sierre club in the Swiss Alps, where he lost a playoff as a 19-year-old in 2008.
Soderberg seemed to have wasted his best chance of victory shortly before the playoff, three-putting from 5 feet on the 17th green to fall into a share of the lead at 14 under.
The Swede ultimately carded a four-under 66 for a 266 total, alongside his playing partners McIlroy (67) and Lorenzo Gagli (67), and was soon joined by Kalle Samooja (67) and third-round leader Andres Romero (70).
But playing the par-four 18th as the first extra hole, Soderberg was the only player to stay on the fairway.
Soderberg, 28, then made his putt from approximately 8 feet out before McIlroy and Samooja missed from closer range.
It was a first European Tour title for Soderberg, whose winner's check more than doubled his career winnings.