Team Sky’s two-time Olympic track gold medallist beat Javier Moreno (Spain / Movistar), Ben Hermans (Belgium / RadioShack) and Tom-Jelte Slagter (Netherlands / Blanco) to the line.
The quartet escaped some carnage on a blind corner during the high-speed descent from the steep Corkscrew Road climb with under 7km remaining of the 116.5km stage from Mount Barker to suburban Rostrevor.
World champion Philippe Gilbert was one of over 20 cyclists either brought down or caught up in the crash which resulted in Frenchman Arnaud Courteille taken to hospital suffering from mild concussion and a suspected broken nose while Italian Giovanni Visconti was to undergo X-rays for suspected broken ribs.
Welshman Thomas delivered a stinging attack on the decisive climb and was in the four-man lead group that formed on the descent.
They held off 11 chasers to contest the stage victory and biding his time in the sprint, Thomas put in an explosive dig to take the ochre jersey with a five-second lead on GC. He said: "I’m really happy with that. I’ve worked hard since the Olympics trying to lose the track weight and I’ve got some good kilometres in over the winter. I wanted to start this year strong. I knew I had decent form but you never know how well everyone else is going. "I always knew that I’d have decent legs on the climb I just wasn’t sure how I’d go. I got a bit excited and attacked a bit earlier on there. With about 400 metres to go I was starting to tie up but fortunately there was that group behind and we were able to work well together. "To get the win is a massive bonus for all the hard work over the winter."