Downing had won the opening stage and finished well yesterday. In terrible conditions, many of the 103 riders opted not to go up the St Patricks Hill which is one of the steepest climbs on the European cycling tour.
Lance Armstrong pulled out before he got to the hill, citing a back problem with Mark Cavendish who won yesterday's second stage also with drew leaving only 47 riders to complete the 185km stage.
Downing knowing he had to finish, attacked with four kilometres to go and was able to fend off defending champion Marco Pinotti plus attacks from a number of Saxo Bank riders.
One rider he could not stop was Lars Petter Nordhaug and the Joker Bianchi rider was first to the line ahead of the yellow jerseyed Downing, who ensured that his second place was enough for his biggest victory of his career so far.
British Champion Kristian House finished 12th.
"I felt good as soon as we came onto the big climb [St. Patrick's Hill] I was really good," said Downing to Cycling News after the race. "I looked across at Pinotti and his tongue was out and everything, but I was there feeling pretty comfortable. This is definitely my biggest result."