Söderqvist completed the 14.3 kilometers in 15 minutes and 28 seconds.
The 22-year-old Swede thus recorded the third win in his professional career. The other two wins were recorded during the Swedish time trial Championships. It was the first time since 2008 that a Swede won a stage in the Danish stage race.
At the last interval, the Danish champion in the discipline, Mads Pedersen, looked like he could finish faster than his Swedish teammate, but on the way to the finish line, the Danish star could not maintain the speed.
Mads Pedersen thus ended up being 14 seconds behind his teammate, which just secured Pedersen third place on the stage, which was enough to defend the overall lead in the race.
The Danish pace specialists Niklas Larsen and Johan Price-Pejtersen finished fourth and fifth.
The Dutch star sprinter Fabio Jakobsen, who has had problems with blood circulation and has not completed a race since March, chose to retire before the start of the race.
The biggest stage in the race awaits on Friday from Svendborg to Vejle. The 227-kilometer-long stage ends in hilly terrain, where classification riders will chase vital seconds.
The race ends on Saturday.