The eighth-seeded van de Zandschulp led 4-3 in the opening set — with Rune serving at 40-15 — when he withdrew due to chest pains.
“This was probably the worst way to win a final,” said Rune, who celebrated his 19th birthday on Friday. “I was obviously expecting a very tough match and he came out very strong. I just wish him all the best, a speedy recovery, and we all just hope to see him back on the court very soon.”
Rune, who stunned top-seeded Alexander Zverev in the second round, did not drop a set at the clay-court tournament. He also ousted Jiri Lehecka, Emil Ruusuvuori and Oscar Otte on his way to his first final.
The 70th-ranked Rune became the third youngest champion in Munich after Guillermo Perez-Roldan won at age 17 in 1987 and successfully defended his title a year later.
Rune is the fifth first-time winner on the ATP Tour this year.
“I’m super happy, of course,” Rune said. “As I said, not the way I want it to end, but if I look through the week, what a week! … To be playing here in Munich and winning my first ATP title in front of such a brilliant crowd, I couldn’t really ask for more.”