The Englishman had been sat on the lead for two days after torrential rain saw the weekend washed out and the event pushed to Monday and reduced to 54 holes.
Excellent scoring conditions greeted the field across St Andrews, Kingsbarns and Carnoustie but nobody could get past Fitzpatrick, who reached 19 under to win by three shots from countrymen Marcus Armitage and Matthew Southgate and defending champion Ryan Fox.
In the team event, Susan contributed three birdies and an eagle in a 59 that got the pair to 35 under and sealed a five-shot tirumph.
Fitzpatrick becomes just the second player to do the individual and team double after Pádraig Harrington in 2002 and 2006, while Susan becomes the second female winner at this event, following Maeve Danaher who won alongside Michael Hoey two years ago.
The victory caps a remarkable fortnight for Fitzpatrick, who was part of Luke Donald's winning Ryder Cup team, earning his first point in his third appearance as Europe triumphed 16½-11½.
The win is Fitzpatrick's ninth individually on the DP World Tour but he admits that winning alongside his mum in the team event is the highlight of the week.
"It doesn't get better than this," he said. "Winning at St Andrews, it's just a very special place. We've been coming here for a long, long time as well and it doesn't get better.
"We played last year and didn't quite play so well and this year she's played fantastic and I played really solid as well. You just couldn't ask for a better week.
"It's amazing. Winning is difficult. I had a chance a few weeks ago in Switzerland and that one hurt a lot. I felt like I had been playing better than I had in the summer.
"This week, it's funny, really, it was kind of a bit of a free-wheeling week and just playing with my mum and trying to enjoy it as best I can and see what happened.
"Then played really well at Carnoustie and just got on a hot run these last two rounds."
Fitzpatrick started the day with a one-shot advantage and was two ahead after putting an approach to six feet at the first but he soon had company in the form of the charging Southgate.
The 35-year-old left himself 12 feet on the first and short putts on the third and fourth, with Fitzpatrick dropping a shot on the second after finding sand off the tee.
The 2022 U.S. Open champion was back ahead with an eight-footer at the third but Southgate put his second to five feet at the par-five fifth and made his eagle putt to hit the top on his own.
Fitzpatrick got up and down for birdie on the same hole and while Southgate holed from 24 feet on the eighth, his rival hit back from 15 feet on the seventh and the duo led by four shots.
They would not have that advantage for long, however, as Kiwi Fox showed he would not let his title go without a fight.
He sandwiched a two-putt gain on the fifth with a long putt on the second and smart approach to the seventh.
Another two-putt birdie after driving the par-four ninth then triggered a hat-trick of gains and when he left himself three feet at the tenth and put a tee-shot to seven feet at the 11th, he was just one back.
Fitzpatrick joined him with a three-putt at the tenth but hit back with a tee-shot to eight feet on the next and the Englishman soon led alone as Southgate bogeyed the 14th after finding sand off the tee and having to play out sideways.
The leader holed a long putt on the 13th and hit an excellent approach into the 15th to lead by three and, while Southgate and Fox both made the most of the short par-four 18th to sign for rounds of 66 and 65 respectively, so did Fitzpatrick to set the target at 19 under.
Over at Carnoustie, however, Armitage was still in with a chance of catching him after starting almost 90 minutes later on the 11th in a shotgun start.
He hit a beautiful approach into his opener, birdied the par-five 12th, left himself 25 feet for eagle at the 14th and hit an excellent recovery after a poor tee-shot at the 17th.
A bogey on the 18th stalled his progress but he made gains at the fourth, sixth and seventh to sit two back with three to play before three-putting the ninth.
Swede Sebastian Söderberg fired the lowest round of the day with a 62 at Kingsbarns to finish at 15 under, a shot clear of Belgian Nicolas Colsaerts, Frenchman Matthieu Pavon, Finn Sami Välimäki and England's Matt Wallace.