Jabeur was aiming to become the first Arab Grand Slam singles champion. However, there was more heartbreak for the Mena tennis icon after her defeat to Elena Rybakina in the final at the All England Club last year and her loss to world No 1 Iga Swiatek at the US Open later in the year.
Vondrousova became the first unseeded woman to win Wimbledon in the Open era.
Vondrousova was a heavy underdog against sixth-ranked Jabeur. But the 24-year-old Czech upset the odds on Centre Court to win her maiden Grand Slam title at the second attempt after losing to Ash Barty in the 2019 French Open final.
Vondrousova joins Jana Novotna and Petra Kvitova as the only Czech women to win a Wimbledon title.
Vondrousova's win completed a remarkable comeback after a spate of injuries stalled her promising career.
Just 12 months ago, she was an injured bystander at Wimbledon, reduced to watching her best friend Miriam Kolodziejova attempt to qualify for the main draw.
Vondrousova's second wrist surgery had ruled the Olympic silver medallist out for six months.
She was the second-lowest ranked player to reach the Wimbledon final - only Serena Williams in 2018 was lower at 181.
Vondrousova climbed up the stands to hug her team in the players' box, while Jabeur sat dejected in her chair.
After receiving the trophy, Vondrousova said: "I don't know what's happening now.
"Ons, congratulations, you're such an inspiration for all of us, I hope you are going to win one day.
"After everything I've been through - I had a cast on this time last year - and now I can't believe I'm holding this trophy."
Jabeur, last year's losing finalist as well, broke down in tears after receiving her runners-up trophy from the Princess of Wales.
"This is very tough. It's the most painful loss of my career," she said.
"Congratulations to Marketa and her team. You are an amazing player, I know you had a lot of injuries and I'm very happy for you.
"It's going to be a tough day for me today but I'm not going to give up. I'm going to come back stronger.
"I promise I'll come back one day and win this tournament."
Under the closed roof, Jabeur drew first blood with a break in the second game when Vondrousova netted a backhand.
But she immediately surrendered the initiative as Vondrousova broke back in the next game.
Jabeur's anxiety was clear as her unforced error total reached double figures in another wild game that gave Vondrousova a 5-4 advantage that she seized to serve out the set.
Vondrousova made it five games in a row when Jabeur's weak forehand gifted her a break in the opening game of the second set.
Breaking twice in three games, Jabeur moved 3-1 up, only to falter again as the ninth break of the match allowed Vondrousova back into the set.
It was an opportunity the Czech was not going to spurn as Jabeur's unforced errors reached 31 by the final game.
Vondrousova remained ice-cool and sealed victory with a perfect volley before falling to the turf in delight.