After winning last week's thrilling first leg on home soil by a 3-2 scoreline, La Viola found themselves a goal behind in Wednesday's reverse fixture at Jan Breydel Stadium courtesy of a first-half strike from Brugge defender Maxim De Cuyper.
Vincenzo Italiano's side were the dominant force in the second half and although they were denied three times by the woodwork, Lucas Beltran comfortably dispatched a controversially-awarded penalty five minutes from time to salvage a 1-1 second-leg draw and send the Italians through to a sixth European final.
Victory for Fiorentina sees them progress to back-to-back Conference League finals and moves them one step closer to seeking redemption after losing last year's showpiece to West Ham United.
As for Club Brugge, they ultimately ran out steam and ran out of ideas in the final third, and Nicky Hayen's men have fallen short of reaching their first European final for 32 years.
De Cuyper wipes out Fiorentina's first-leg lead
Both sides cancelled each other out in the opening exchanges and although there was little goalmouth action, Club Brugge showed a greater level of attacking intent and were eventually rewarded in the 21st minute.
The hosts' opener came from an unlikely source but as welcomed one, as left-back De Cuyper - starting due to the injured sustained by Bjorn Meijer in the first leg - met an inviting cross into the six-yard box from Hans Vanaken before glancing the ball in unorthodox fashion into the far corner.
Fiorentina responded well and should have scored just a few minutes later when Nicolas Gonzalez was sent through on goal, but the Argentine's tame effort was saved by Simon Mignolet before Andrea Belotti dragged the rebound narrowly wide.
Club Brugge were then presented with a decent chance to double their second-leg advantage when Nikola Milenkovic lost his footing on the left channel, allowing Igor Thiago to drive forward and tee up Michal Skoras from 10 yards out, but Fiorentina's Dodo reacted first to make a vital interception.
The hosts had the woodwork to thank 10 minutes before the break, with Christian Kouame left perplexed by how his venomous 20-yard half-volley smacked the underside of the crossbar and bounced off the line before the ball was cleared away from danger.
Fiorentina fightback rewarded with late winner
A firework and pyro show took place in the stands as they players walked out for the second half, and just 30 seconds after blowing his whistle for the restart, referee Halil Umut Meler opted to halt the contest for a few minutes to allow the thick cloud of smoke to clear.
Once play resumed, Brugge made a positive start and Fiorentina were caught napping when defending a corner, as they allowed an unmarked Denis Odoi to meet De Cuyper's corner. However, the former Fulham man mistimed his leap at the near post and the ball bounced off the back of his neck before the danger was dealt with.
Fiorentina gradually grew back into the tense contest and could sense that Brugge were beginning to tire, but they were struggling to carve out many clear-cut chances to test Mignolet. However, La Viola found their groove as soon as Italiano freshened up his side with a couple of changes in the final half-hour.
Captain Cristiano Biraghi tried his luck from two free kicks - his first sailed over before his second from around 25 yards out smacked the top of the crossbar, just a minute before Kouame rose above the Brugge backline to thump a powerful header against the post after meeting Gonzalez's curling cross from the right.
It was one-way traffic in Fiorentina's favour heading into the final 10 minutes and their persistence in the final third eventually told, although their decisive goal came about in somewhat controversial circumstances.
Brugge defender Brandon Mechele was penalised after raising his knee towards the head of substitute M'Bala Nzola, even though he made minimal contact with the Fiorentina attacker, who went down far too easily.
Nevertheless, Beltran was the man tasked with firing Fiorentina into the final, and he just about squeezed his spot kick beyond Mignolet's outstretched right arm and into the bottom-left corner, sparking pandemonium in the away end.
Pietro Terracciano then came to the rescue deep into stoppage time as he made a magnificent one-handed save at full stretch to prevent Vanaken's deflected strike from nestling into the bottom corner.
Fiorentina eventually held on for a deserved aggregate victory and they will face either Olympiacos of Aston Villa at the Agia Sophia Stadium in Athens on May 29.
Both teams will now turn their attention back to domestic duties, with Fiorentina hosting Monza in Serie A on Sunday, the same day Club Brugge do battle with Union SG in the Belgian Pro League.