The unseeded Krejcikova beat Anastasia Pavlyuchenkova 6-1 2-6 6-4 in the battle of two first-time Major singles finalists on Court Philippe-Chatrier.
Krejcikova said her former coach and compatriot Novotna, who died from cancer aged 49 in November 2017, was always in her thoughts as she embarked on a surprise, glorious run at Roland Garros.
The 25-year-old pointed to the sky as she delivered a poignant tribute to Novotna after becoming the first Czech woman to win the title in Paris since Hana Mandlikova in 1981.
She said of the 1998 Wimbledon champion: "I was going through a really hard time when Jana passed away, I was with her most of the time. Her last words were pretty much 'just enjoy it and try to win a grand slam'."
Krejcikova added: "I know from somewhere she is looking after me and all this what happened in the last two weeks is pretty much because she is looking after me from up there.
"It is amazing I had the chance to meet her and she was an inspiration. I hope she is really happy and I am extremely happy."
Ranked No.114 when the WTA Tour returned last August after a coronavirus-enforced shutdown, the surprise package is the sixth consecutive maiden Major champion to be crowned at the French Open.
Krejcikova, a winner of five grand slam doubles titles with another up for grabs on Monday (AEST), was pinching herself after lifting the Suzanne Lenglen Cup.
"I want to thank all of them – my coach, my physio, my friends and everyone back home. My family, my mum and dad, my brothers, my niece and nephew. It's nice to see everyone," she said.
"It is hard to put into words because I cannot believe what just happened. I cannot believe I actually won a grand slam."