After a frantic start to the second longest stage of the race, Deignan rode hard to force his way into the day's 14-man move as the peloton headed along the coast for Savona.
The group which also included Ireland's Nicholas Roche combined well, but with 50km to go Deignan suffered an unfortunately timed puncture.
The Donegal man did fight his way back with the group moving at a flat-out pace.
By then the peloton were almost in sight and the final climb saw a regrouping at the front with 24km left to run.
Philip is 83rd in General Classification while Cadel Evans stayed safe with the help of his BMC Racing team-mates to retain his 57-second race lead heading into Thursday's time trial.