The players took the court almost six hours late after a day of wild weather in the German capital, which forced the tournament to be evacuated for several hours.
The 21-year-old claimed the opening set and maintained control in the match despite losing the second set against the 2024 champion to claim a second career title and a first at the WTA 500 level.
Czech Noskova is set to climb into the WTA top 10 for the first time in her career when the new rankings are released next week.
"(This is) very incredible and unforgettable for me," Noskova said.
"It's my second title, so like I said, you never forget the first ones, but you always never forget the second ones as well."
The result was a setback for 32-year-old Pegula, who has never won a Grand Slam, just a week out from the start of Wimbledon.
Pegula eliminated world number one Aryna Sabalenka in the semi-finals on Saturday to reach the final in Berlin for a second time.
Noskova breezed past Filipina qualifier Alexandra Eala in the semis and continued her strong form to break Pegula twice and claim the opening set.
Pegula found her feet in the second, breaking her opponent once to take it 6-4, the first time Noskova had dropped a set so far this tournament.
The American looked to have a footing in the match, but Noskova broke early in the deciding set to drag the match back into her favour.
Noskova is set to remain in Germany in the coming week to take part in the Bad Homburg tournament, another key Wimbledon preparation event, before travelling to England.