The Dane's second stage victory of this year's race also saw him take back the overall leader's jersey from Primoz Roglic.
Pedersen (Lidl-Trek), who won the opening stage, took to the front in the sprint finish and held off Strong (Israel-Premier Tech) by half a wheel, with Venezuela's Orluis Aular (Movistar) finishing third, as he did in stage one.
The stage victory gave Pedersen a 10-second bonus, which means he retakes the pink jersey from race favourite Roglic, having begun the day one second behind the Slovenian.
"Wow, to have two stage victories already and now back in the pink that's exactly what we wanted today," Pedersen said.
The stage, a 160-km ride starting and finishing in Vlore and the last of three stages in Albania, was dominated by an early breakaway which included Saturday's time-trial winner, Briton Joshua Tarling (INEOS Grenadiers).
Having opened up a gap of over three minutes on the peloton, the six-man group started to splinter as the bunch began to eat into their lead, with the riders all back together for the final 16km to set up the sprint finish.
Bahrain Victorious controlled the front of the group in the final kilometres, looking to set Antonio Tiberi up for the win, but in the closing stages, Pedersen's colleagues Mathias Vacek and Giulio Ciccone had the Dane perfectly positioned.
Pedersen attacked early with Strong following but nobody was going to deny the new race leader another victory, and after relinquishing the overall lead to Roglic on Saturday (local time), he will now wear the pink jersey when the race reaches Italy.
"This was the plan from this morning to put a good pace on the long climb to control it for ourselves and give me a breather," Pedersen said.
"Then from the climb on it was controlling as far as we could and it was exactly as we wanted and then Ciccone and Vacek there doing an amazing lead out."
After Monday's rest day, Tuesday's stage four will be a flat 189-km ride from Alberobello to Lecce.
