England were dealt a huge blow as they lost Chelsea's Lauren James following her stamp and subsequent red card towards the end of the second half, but somehow took it to penalties at 0-0.
Nigeria had 20 shots compared to England's 12 in the game, with the Lionesses' attacking threat diminished even before James was given her marching orders.
But despite all of that, somehow, it was England's day.
Bayern Munich's Georgia Stanway - who has been perfect from the spot for England, converting seven out of seven spot kicks - stepped up first, but fired well wide of the left hand post.
Nigeria's Desire Oparanozie then produced a carbon copy of Stanway's miss, returning the shootout to a level playing field.
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Beth England then converted, going straight down the middle. before Nigeria's Michelle Alozie - who was stamped on by James - fired over the bar.
Rachel Daly then fired into the top corner, before Ajibade netted her country's first, before Alex Greenwood followed up with a tidy finish.
Nigeria's Christy Ucheibe made no mistake either.
European championship and Finalissima winning goalscorer Chloe Kelly capitalised on Nigeria's errors, though, smashing the Lionesses' final penalty into the top corner to send them into the quarter-finals.
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The England fans behind the goal went wild as the Lionesses celebrated, with the team also making time to console their opponents who gave it their all in the 120 minutes.
Sarina Wiegman's side are now on track to equal their run in the 2019 World Cup that saw them reach the semi-final before falling to defeat to the United States, who were knocked out of this year's tournament on Sunday in controversial style.
England will play either Colombia or Jamaica on Saturday.
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