The tie was a repeat of last year's showpiece match at the WTA 1000 clay-court tournament.
Sabalenka, the back-to-back Australian Open champion, won the 2023 final in three sets - but it was her Polish opponent who triumphed this time.
Swiatek saved three championship points to secure her 20th career title and deny the Belarusian a third success on the red clay of the Spanish capital.
The match was the first meeting of the season between the top two in the women's rankings and it lived up to expectations, the longest encounter between the two grand slam champions at three hours 11 minutes.
"It is always a challenge playing against you Aryna, so thanks for motivating me and forcing me to be a better player, Swiatek said on court after her triumph.
Sabalenka paid tribute to Swiatek, saying: "Congrats on another great tournament Iga, you are doing an incredible job and hopefully next year it (title) goes to me.
"It was a great match and a long one, hopefully we will recover well for the next tournament."
Swiatek will seek her fourth French Open title later this month as the two-time defending champion at Roland Garros.
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