The Italians came into the second leg with a one-goal lead but that were pegged back after Maxim De Cuyper scored in the first half. However Lucas Beltran stepped up with a late penalty to send his team into the final.
Fiorentina are through to their sixth-ever European final, after a late penalty secured their opportunity to play for the UEFA Europa Conference League title.
Their 4-3 aggregate victory was secured by Lucas Beltran, who converted a penalty five minutes from time as the game appeared destined for extra time.
The visitors were the better team throughout and missed a number of chances. Christian Kouame hit the bar in the first half and the post in the second, while Cristiano Biraghi also curled a free-kick onto the bar.
It was Club Brugge that went ahead in the match in the 20th minute, when Maxim De Cuyper turned in a cross from Hans Vanaken.
From then on Fiorentina took control of the match, but still required a smart save from Pietro Terracciano to keep out Vanaken in injury time.
Fiorentina will play either Olympiacos or Aston Villa in the final in Athens on 29 May, and have the chance to avenge their defeat in the final against West Ham United last year.
TALKING POINT – CAN FIORENTINA TAKE THE FINAL STEP?
Last June their hearts were shattered as Jarrod Bowen sprinted through to score a goal that went down in West Ham folklore.
The thought of losing again is almost unbearable. Fiorentina won the inaugural European Cup Winners Cup in 1961, but possess the unwelcome record of having lost in the final of not just their defence of that title the following year, but the 1957 European Cup Final and the 1990 UEFA Cup Final alongside their defeat in Prague last June.
That smorgasbord of failures is a lot of scratches to itch, as the club go in search of their first European trophy for 63 years. Either Olympiacos or Aston Villa will be one opponent, and the weight of their own history another.
PLAYER OF THE MATCH – NICOLAS GONZALEZ (FIORENTINA)
He missed a gilt-edged chance when through one-on-one with Simon Mingolet, but outside of that Gonzalez was the main creative outlet for the visitors. His improvised cross helped win the penalty that put his team in the final, a match in which he could have a key influence.
