Zverev, a runner-up in 2020, prevailed 6-3 7-6 (7-4) in Saturday's opening semi-final at Bercy to set up a showdown with either 2018 champion Karen Khachanov or 15th-seeded home favourite Ugo Humbert.
Victory on Sunday would give Zverev a seventh Masters title and also move him past top-ranked Jannik Sinner for most wins on the ATP tour this year. They are tied on 65.
Rune saved one match point with a brilliant cross-court forehand winner, but the third-seeded Zverev held his nerve on the next with a crisp backhand volley at the net.
"I feel like I made it a little difficult for myself but he is a champion. It is probably his favourite tournament and favourite court," the 27-year-old Zverev said.
"I am happy to be in my second final here, I am looking forward to it."
Zverev was mostly in control against Rune in their fourth career meeting and first on indoor hard courts.
The French Open runner-up improved to 3-1 overall against his rival, who won the Paris Masters in 2022 by stunning Novak Djokovic in the final.
Rune, who knocked out Alex de Minaur in the quarter-final, saved a break point in his opening service game as he struggled from the back of the court.
Zverev broke him in the fourth game when Rune's two-handed backhand went out, and he held serve for a 4-1 lead in a commanding first set, clinching it when his opponent returned long.
He broke the Dane to serve for the match for the first time at 5-4, but Rune hit straight back to level.
A long 11th game saw both players miss chances and it went to a sixth deuce before Rune finally won it with a backhand volley at the net.
That was the end of his resistance and Zverev was untroubled in his next service game and in the tiebreaker as he ended Rune's already slim chances of making the season-ending ATP Finals in Turin.
The big-serving German is bidding for his second title of the year and 23rd overall.
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