The two played for three hours and 16 minutes on Sunday (AEST) – the longest WTA final of the year – with Kerber eventually sealing it 7-6 (7-5) 6-7 (0-7) 7-6 (7-5) to win her first clay court trophy in more than six years.
In their only previous meeting in 2020, Juvan upset the former world No.1 at the French Open, and the 21-year-old gave Kerber another scare here.
There were three breaks of serve each in the first set, with neither able to take control, before the German edged the first of the trio of tie-breaks.
Juvan and Kerber exchanged two breaks each in the second, though it was the Slovenian who was finding more opportunities, forcing the No.2 seed to save eight further break points across the set, before dominating the second breaker.
Neither was able to pull away in the third, with Kerber breaking early, before Juvan hit right back. It felt inevitable that the third set would follow the first two in going to a tie-break, and so it proved.
Kerber finally put her determined opponent away and paid tribute to the world number 81 in her maiden WTA final during her on-court interview, saying: "Well done Kaja, you played a great week and also a tough final... I wish you all the best in Paris [the French Open] so good luck there."
In the final of the Morocco Open, Martina Trevisan eased to her first WTA title at the expense of Claire Liu in just more than 90 minutes.
The Italian dominated her opponent in a 6-2 6-1 victory after winning 63.0 per cent of her first serve points and saving nine of 10 break points.
Liu just could not get going, only winning 38.7 per cent of her own first serve points as she was unable to contain Trevisan, who becomes the second first-time champion in 2022 after Anastasia Potapova in Istanbul.
Trevisan dedicated the win to her father, saying: "I would like to dedicate this trophy to my dad. He can't see me in this moment but I know he would be very proud of me. He is a fighter like me during this week, but during his whole life - so this is for you, dad."