The first shake-up in this year's race coincided with its arrival home in Italy following the opening three stages in Bulgaria, and after Aular hit the front ahead of Ciccone, Narvaez came from behind and left the Venezuelan in his wake.
Narvaez had previously won Giro stages in 2020 and 2024 but had not raced since a crash in January at the Tour Down Under in Australia.
"It's really big for me, coming from three months training in Ecuador," Narvaez said.
"I want to say thanks to my family, my wife, my team. They've been a great support in this time."
The 138-km ride from Catanzaro to Cosenza only kicked into gear when the stage reached the foot of the long climb to Cozzo Tunno, 80km into the race, and the peloton was broken up, leaving a reduced bunch of 42 riders to fight for the stage.
After a relatively sedate three days in Bulgaria, apart from crashes on the opening two stages, Aular's Movistar team set the pace on the ascent, quickly reeling in a six-rider breakaway and leaving most of the sprint favourites behind, along with Guillermo Thomas Silva.
Silva had worn the leader's jersey since winning stage two, but the Uruguayan had no answer on the climb and finished the stage over 12 minutes down on the winner.
Narvaez's teammate Jan Christen was first to make a move when the riders came to the 1.5-km run-in to the finish, but having taken valuable seconds in the intermediate sprint, this time his dash was in vain.
"Jan is a great guy, he was trying to take the pink jersey," Narvaez said.
"He's a young guy, he needs to learn how to race. He did a great final and in the end for me it was just waiting for the sprint."
Christen did move into second overall, four seconds behind Ciccone (Lidl-Trek), with the Italian snatching pink thanks to his bonus seconds at the finish and in the earlier sprint, which will ease the disappointment of not winning his fourth Giro stage.
Australian Kaden Groves abandoned the race during Tuesday's stage, still suffering after his involvement in the crash at the end of stage one.
Wednesday's stage five is a 203-km hilly ride from Praia a Mare to Potenza.