Gilbert won Stage 12 of the Giro d'Italia a week ago, when he charged out of the peloton in a driving rainstorm on the uphill finish at Monte Berico in Vicenza.
The BMC rider's second victory came after he soloed out of a breakaway that included eventual fifth place finisher, team-mate Amaël Moinard.
Gilbert's attack came 19 kilometres from the finish of the 170km stage. He crossed the line 47sec in front of Francesco Bongiorno (Bardiani-CSF Pro Team) and 1min 1sec ahead of Sylvain Chavanel (IAM Cycling), who won a six-up sprint for third.
"This is definitely one of my most satisfying victories because I had time to enjoy it in the final three or four kilometres," said Gilbert. "I heard on the radio from [BMC Racing Team Sport Director] Valerio Piva that I had a minute on the chasers. With a minute, I knew the stage was won."
Gilbert and Moinard were part of an original group of 12 which escaped the peloton about 45 kilometres into the stage. They rapidly built a lead that peaked at nearly 13 minutes before the race headed up the Monte Ologno, the day's major climb.
Moinard was part of a group of four that crested the summit about a minute ahead of a chase group that included Gilbert. On the descent, Gilbert's group caught the leading quartet. The former world road champion did not waste any time venturing off on his own.
"This morning on the bus, we talked about how the breakaway might have a chance. At the foot of the climb, the rest went full out. But I knew I had to ride my own tempo. When I made contact with the front group, I started to attack immediately. Yes, I took risks on the descent. But you have to if you want to win a stage in the Giro." - Philippe Gilbert.
Gilbert led by 46 seconds with five kilometers to go and had plenty of time to celebrate winning two stages in a grand tour for the third time in his career. In 2012, he won two stages of the Vuelta a España (Stage 9 and 19). In 2014 he won Stages 3 and 19 of the Vuelta.
BMC sport director, Fabio Baldato said the race went precisely according to the team's pre-race plan, which was to get two riders into the breakaway.
"We are really happy. This was really great," said Baldato. "It was not easy to make the breakaway. It was a 49 kilometres-per-hour average the first hour, which was a really hard start. Silvan Dillier, Brent Bookwalter, Rick Zabel and Marcus Burghardt all tried to make the breakaway. Phil and Amaël made the race hard, they made the attack and they forced the breakaway. For us, it was perfect."
Race leader Alberto Contador (Tinkoff-Saxo) finished 12th on the stage and increased his advantage over second-placed Mikel Landa (Astana) to 5min 15sec.