Krejcikova had not won a singles title since her third triumph of 2021 in Prague last July, but ended her drought with a 6-2 6-3 defeat of the top seed.
The Czech ended the home favourite's hopes of being crowned champion in a showpiece match that was over in an hour and 21 minutes.
Kontaveit had won 24 consecutive indoor matches on hard courts, but she was no match for the 2021 French Open champion.
Krejcikova won 71 per cent of points on Kontaveit's second serve, breaking twice in the opening set and three times in the second.
She drew first blood to go 4-2 in the first following precise groundstrokes off both wings, then broke for a second time to seal an opening set in which Kontaveit made 13 unforced errors.
World number four Kontaveit responded with a break in the opening game of the second set, but failed to back that up with a hold.
Kontaveit had the initiative again at 3-1, but there was a sense of deja vu as her opponent broke straight back and served out the match after moving 5-3 in front with another break.