Jhon Arias and John Kennedy got the goals at King Abdullah Sports City to send the South American champions into Friday's final, where they will face either Manchester City or Urawa Red Diamonds.
Arias's goal came from the penalty spot after Marcelo had been brought down inside the area 19 minutes from time, and Kennedy then sealed his side's progress with a second late on.
Fluminense, and Arias in particular, may have been beginning to worry that it would not be their night after the Colombian hit the woodwork twice in the first half.
However, it was third time lucky as he made no mistake from the penalty spot after Percy Tau had brought down Marcelo in the box.
Tau had a glorious chance to make immediate amends for conceding that penalty when he was picked out by a defensive-splitting long pass forward by Hussein El Shahat moments later, only to glance his header straight at Fabio in the Fluminense goal.
The Brazilian keeper was needed again shortly afterwards, this time to keep out Taher Mohamed, before Mohamed El Shenawy kept his side in it at the other end with a big save to deny German Cano when one on one.
Fluminense's second goal did not take too much longer to arrive, though, with Kennedy - the man who scored the winner as the Rio outfit won the Copa Libertadores for the first time ever last month - slotting a confident finish into the bottom corner from inside the area.
Only a smart El Shenawy save to deny Cano again prevented things from getting even worse for Al Ahly late on as they once more failed to make the final of the competition, extending their unwanted record of having featured at nine Club World Cups without ever reaching the final.
Fluminense, meanwhile, will have the chance to become the first non-European winners of the tournament since fellow Brazilian side Corinthians in 2012, and they will learn their opponents when Man City face Urawa Red Diamonds on Tuesday.