Swiatek has now lost only two out of 26 grand slam matches since moving to world No.1 in April last year and the 22-year-old became the youngest woman to bag consecutive trophies at Roland Garros since Monica Seles, who won from 1990-92.
The US Open champion also joined Seles and Naomi Osaka as the only women in the Open Era to emerge victorious in each of their first four major finals, but she was made to work for it by a determined Muchova.
"First of all congratulations to Karolina," said Swiatek, who became the first woman to successfully defend the Roland Garros women's singles title since Justine Henin in 2007.
"To my team, sorry for being such a pain in the... I'll try to do better.."
Swiatek worked the angles superbly from the baseline and blazed ahead 3-0 before world No.43 Muchova settled the nerves, got on the board and eventually forced a decider in a thriller match.
Muchova was brimming with self-belief, having edged Aryna Sabalenka in a three-setter in the semi-finals, and went ahead in the final set, but Swiatek shrugged off the early break and wrestled back the momentum by winning three straight games.
The top seed dropped serve in the seventh game but broke back instantly and produced a tight hold to inch closer to the title, which she wrapped up when Muchova double faulted.
That sparked emotional scenes on centre court as Swiatek shed tears of joy before joining her family in the crowd for a celebration.
In a moment that set social media alight later, she dropped the lid of the cup as she waved the trophy in the air.
For Muchova, it was a first defeat against a player ranked in the top three in six meetings.
"I'll keep it short because it's bit emotional," she said, with tears flowing and the crowd chanting her name. "It was so close yet so far but I played one of the best, Iga. I want to congratulate you out loud again and your team.
"To my box. When I look at those people, I feel I'm the winner. Thank you. I hope this is only the beginning. We've come a long way."
Swiatek's third win in Paris put her level with modern day three-time champions Serena Williams, Monica Seles and Arantxa Sanchez Vicario.
Fourth seeds Ivan Dodig and Austin Krajicek later won the men's doubles title as the Croatian-American pair defeated Belgians Sander Gille and Joran Vliegen 6-3 6-1.
