England chased down a challenging target of 223 in the third and final T20 to come from 1-0 down to take the series 2-1.
Morgan dealt exclusively in sixes for his boundaries, clubbing seven of them as England finished on 226-5 with five balls to spare for a five-wicket win.
South Africa made 222-6 at SuperSport Park after choosing to bat first.
Moeen Ali hit the four down the ground to seal the win for England but there was no doubt Morgan won it for his team.
The key partnership was Morgan's stand with Ben Stokes, which reaped 61 runs from 27 balls.
England needed 53 from the last four overs but Morgan launched two sixes in the 17th over, Stokes matched that feat with two maximums in the 18th over, and Morgan did it again with two sixes in the 19th.
Stokes, who scored 22 from 12, was caught on the boundary at the start of that second-to-last over and England still had work to do.
Morgan eased the tension by connecting with two low full tosses from Lungi Ngidi off successive balls. The first disappeared into the crowd over mid-wicket and the second went flying over the square leg boundary.
England ultimately only needed one run off the last six balls as Morgan's masterclass made it an easy win at the end.
"Extremely satisfying, particularly when I'm there at the end," Morgan said. "Nice note to end this tour on ... it's a hugely productive series for us."
England's 226-5 was its second-highest total batting second in T20s and the fifth-highest ever for a team batting second. Morgan's 50 came off 21 balls, equaling his own record set last year in New Zealand for the fastest T20 half century by an England player.
There were two other half centuries at the top of the order - 57 off 29 by Jos Buttler and 64 off 34 from Jonny Bairstow - to help England chase down what seemed a daunting target.
Play was briefly interrupted early in England's innings when climate activists wearing superhero costumes invaded the field, while others climbed a floodlight pylon to display a giant bright yellow banner.
The activists were protesting against air pollution in South Africa. Greenpeace Africa claimed responsibility on its Facebook page.
Earlier, Heinrich Klaasen, a surprise selection for South Africa, top-scored for the home team with 66 off 33 at his home ground and Temba Bavuma made 49 off 24.
The pitch was expected to be high-scoring and it didn't disappoint. Sixes flew in all directions, 13 in the South African innings and 15 in England's.
The victory gave England a winning end to the tour at the SuperSport Park ground in Centurion where it started with the first test in December.
England came from behind in every one of the three series, fighting back to win the test series 3-1, to draw the ODI series 1-1, and to win the T20 series 2-1.
The T20 success will be especially welcome for England with the 20-over World Cup in Australia in October and November. England lost to the West Indies in the final of the last T20 World Cup in 2016.