The Copa Libertadores champions will face the winners of Manchester City's semi-final against Japan's Urawa Reds on Tuesday in Friday's final in Jeddah.
It was a compelling encounter, with an aggressive Fluminense dominating possession, but often being exposed by Al Ahly's counterattacks.
Colombia winger Arias was a constant menace, running up and down the right channel and hitting the post twice in the first half.
However, Africa's champions Al Ahly wasted several opportunities, using the speed of Kahraba and Percy Tau to launch quick counters.
Kahraba was denied from two clearcut early chances, first by Samuel Xavier who made a heroic goalline clearance in the 19th minute, while goalkeeper Fabio made a brilliant one-handed save to palm round the post a close-range header right before the break.
Coached by Brazil caretaker manager Fernando Diniz, Fluminense got back on top in the second half but their goalkeeper Fabio made another critical save from a Tau counter.
Fluminense finally managed to break the deadlock thanks to former Real Madrid full-back Marcelo, who nutmegged a defender, hitting the ball through his legs, to get into the box before being fouled from behind.
Arias slotted the penalty just inside the right post and out of the reach of goalkeeper Mohamed El Shenawy in the 71st minute.
"I always try to do something different (the nutmeg). I've always tried in my whole career," Marcelo told Brazilian TV Globo.
"At that moment, the game was in deadlock. I didn't even think about a nutmeg, it happened, I thought about dribbling to get inside the area.
"So I managed to get in front of him and he fouled me... It wasn't thought out, it came on the spot and it was nice."
Al Ahly had a chance to level one minute later, but Tau missed a sitter, heading into the goalkeeper's hands from point-blank range.
As Al Ahly tried to push for the equaliser, they were left exposed and Fluminense took advantage with substitute Kennedy adding a second in the 89th minute with a strike to finish off a counterattack.
