Morgan scored 17 in the fifth T20I between England and New Zealand, which was reduced to a 11-overs-a-side contest due to rain on Sunday, to cross the milestone.
Chasing New Zealand's total of 146-5, Chris Jordan smashed a six and a four to score 12 from the remaining three deliveries to take his team to 146-7 and force the super over.
Following the controversial ICC World Cup 2019 final, this was the second time both the teams played a super-over.
It was a series decider, it went down to the wire, it was England and New Zealand and it had to be a super over and this time, England were more convincing in winning it. Eoin Morgan and company won the match and clinched the series in good measure.
New Zealand fell nine runs short, losing one wicket for eight runs.
Within the match, England received the toss and requested New Zealand to bat first.
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With New Zealand needing 10 runs from the last two balls Guptill could only manage a single from the first ball he faced and the match was over. It was a rain-curtailed match and the hosts got off to a smashing start courtesy openers Martin Guptill and Colin Munro as they raced along to 83 runs for the first wicket.
England's Chris Jordan reacts after hitting a four from the final delivery and forcing a Super Over in Auckland.
The Black Caps were without rested skipper Kane Williamson, who will return for the two-test series starting later this month. You feel a long way away from everywhere, it doesn't have the hype of an Australia or India series, but they are a brilliant side, and it's a great but tough place to play cricket.
Bairstow would fall with the total on 100, attempting to uppercut Neesham, he merely got a thin edge through to wicketkeeper Seifert, who stumped Curran for 24 off 11 from Mitch Santner's wide. Martin Guptill, Colin Munro and Tim Seifert tore the Brits' bowling apart with some brutal strokes.
Tim Seifert also made a significant contribution for the Black Caps by notching up 16 balls 39 runs. Having scored 47 (18) with the help of two fours and five sixes, opening batsman Jonny Bairstow was the pick of the batsmen for the visitors.