Bradley Wiggins' team-mate from Belarus finished four seconds ahead of Vini Fantini-Selle Italia's Mauro Santambrogio.
Vincenzo Nibali (Astana) and Tour de France champion Wiggins were next over the line, a further 15 seconds back, and they move to fifth and fourth respectively overall.
Tuesday morning's stage one winner Maxime Bouet regained the overall lead from Josef Cerny of CCC Polsat. The duo were part of an eight-man break that finished nearly seven minutes ahead of the peloton.
Bouet is 3:48 ahead of Wiggins who has a nine-second advantage over Italian Nibali following Sky's victory in Tuesday afternoon's team time trial.
“It’s about preparation for the Giro and it was a really hard climb today. I thought maybe I could try to make an attack and see what happened," Siutsou, who is second on GC at 3:19, said.
"A couple of riders followed me but didn’t really want to ride so I just kept pushing a little bit more and tried to control my power. Astana tried to close it down but when I saw that there was 5k to go and the gap of just over 30 seconds I tried to push a little bit harder, but not to go to the very maximum as I wanted to try and keep something for the final kilometre in case someone closed me down.”
Gregor Gazvoda (Champion System Pro Cycling Team), Filippo Savini (Ceramica Flaminia - Fondriest), Tomas Aurelio Gil Martinez (Androni Giocattoli), Michael Schwarzmann (Team Netapp - Endura) and Marco Coledan (Bardiani Valvole - CSF Inox) made an attack stick just before the quarter point of the 224.8km stage from Sillian.
They built up a 6:20 lead on Austrian roads before Savini left his fellow escapees on the 17km long category-one climb of the Passo Lavaze.
But he was caught in the valley by the other four breakaway riders before Coledan attacked ahead of the stage-ending, category-one ascent.
Coledan was the only man in front of the peloton when they began the 14km long finishing ascent but his three-minute advantage was quickly whittled down on the climb with ramps up to 10 per cent and he was caught with 10km remaining.
Siutsou then linked up with Pierre Rolland (Europcar) and Stefano Pirazzi (Bardiani Valvole-CSF Inox) at the front with Wiggins sitting behind in a peloton that was whittled down to under 30 riders halfway up the climb.
Rolland was the first to crack and then Siutsou dropped Pirazzi to lead alone. Nibali was attacking behind and although Cadel Evans managed to ride his way back to the group on one occasion, the 2011 Tour de France champion was unable to deal with a second turn of pace.
Wiggins calmly rode himself back on to Nibali's wheel on both occasions before Santambroggio went off in pursuit of Siutsou inside the final 2km.
He was unable to overhaul him, however, and stayed on his wheel to the line, finishing nine seconds ahead of the fading Domenico Pozzovivo (Ag2r La Mondiale) with Evans 46 seconds behind the stage winner in tenth.
The 37th edition of the four-day, five-stage 2.HC event sees most of the favourites for next month's Giro d'Italia test their legs and concludes with a second summit finish on Friday.