The big hitting Belgian entered the day in a share of the lead with Frenchman Matthieu Pavon and the duo played out an enthralling battle right to the last in Vilamoura.
Pavon was in cruise control over the first 11 holes but found water three times on the way home in a 70 and Pieters took advantage.
The 29-year-old finished at 19 under, two shots clear of Pavon and Danish pair Lucas Bjerregaard and Nicolai Højgaard, who finished with rounds of 66 and 64 respectively.
Højgaard shared the lead in the closing stages as he carded the lowest round of the day but bogeyed the last, while 2017 champion Bjerregaard birdied the 18th to ensure he moves into the top 100 on the Race to Dubai Rankings in Partnership with Rolex and secures his card for 2022.
Pieters had no concerns over his playing privileges but made certain he will play at the season ending DP World Tour Championship, Dubai for the seventh consecutive season.
He had been a picture of consistency coming into this week, with 12 made cuts from 15 events on the 2021 Race to Dubai but his best finish had been a tie for ninth.
He claims his first win since the 2019 D+D Real Czech Masters and moves back into the top 100 on the Official World Golf Ranking in the process.
"It feels amazing," he said. "It felt like a long time between victories but (caddie) Adam and I worked so hard and it felt like a deserved one.
"Two years is a long time. I’ve had a child in the meantime, who talks and runs around, it does feel like a long time.
"I was going into this week and next week with my back to the wall. I had nothing to lose but everything to gain. I’ve never missed the end of the Race to Dubai and really didn’t want to miss it. I didn’t care if I finished first, second or third. I just wanted to get there, but winning is amazing."
Pieters failed to get up and down from a bunker at the first to hand Pavon the lead and the advantage was two after an eight foot birdie on the fourth.
A poor tee shot on the par five fifth had Pieters struggling but he got up to the side of the green and chipped in for an eagle and a share of the lead, although Pavon got up and down from the sand on the same hole to edge back ahead.
A 25 footer from the fringe at the eighth again had Pieters in a tie but Pavon followed him in from 20 feet and the final group were separating themselves from the field.
Pavon put an approach to eight feet on the tenth for another birdie and with Pieters failing to respond from similar distance, the gap was two.
But it was all change at the 12th as Pavon put two balls in the water for a triple bogey eight and a Pieters birdie from 12 feet in the fringe meant the 2016 Ryder Cup star led by two after a four shot swing.
Pavon produced the perfect response with a tee shot to six feet at the next but gave the shot back with a three putt on the 14th.
Pieters found water off the tee at the same hole for a bogey of his own and all of a sudden Højgaard was only one back.
The 20-year-old holed from 13 feet at the second and 21 feet at the third before taking advantage of the fifth to turn in 32.
Approaches to inside ten feet at the tenth and 11th edged him further up the leaderboard and a 25 footer at the 13th and a tee shot to 11 feet at the 16th had him at 17 under.
That was alongside Pavon but the Frenchman's roller coaster continued as he holed a ten footer at the 15th to rejoin the lead, where he soon had Højgaard for company again after a two putt birdie on the par five 17th.
The duo then stuttered, however, with Højgaard bogeying the last after finding sand off the tee and Pavon doing the same on the 17th after hitting water with his second.
That meant that Pieters' stunning iron to 20 feet at the 17th and resulting two putt birdie gave him a two shot lead heading up the last, with a 20 foot putt for par at the 18th putting the icing on the cake.
Bjerregaard holed a 30 footer on the first and hit a smart approach into the second but a bogey on the sixth saw him turn in 34.
Impressive putts on the tenth and 11th were followed by an approach to three feet at the 14th but a bogey on the 16th ended his chances before he made a two putt birdie on the 17th and holed a 40 footer on the last.
Italy's Nino Bertasio and Englishman Matthew Jordan finished at 13 under, a shot clear of another Italian in Francesco Laporta and two ahead of Spaniard Adri Arnaus, England's Richard Bland, Australian Min Woo Lee and Frenchman Victor Perez. European Tour