The Lionesses had Lauren James sent off late on in normal time.
But they saw out extra time before prevailing in a tense shootout as Chloe Kelly sent her team through to a meeting with Colombia or Jamaica.
Nigeria came close to taking the lead when Ashleigh Plumptre’s left-footed shot from the edge of the area crashed off the bar.
She then saw Mary Earps save a follow-up effort after England had failed to clear.
The Lionesses thought they were going to have a chance from the penalty spot just after the half-hour mark.
This was following Rasheedat Ajibade’s challenge on Rachel Daly but the referee changed her decision following a VAR review.
Uchenna Kanu headed wide from a corner in the second half before Nigeria goalkeeper, Chiamaka Nnadozie produced a fine reaction save to keep out the unmarked Daly’s header from a corner.
James was sent off with three minutes remaining following a VAR review after standing on Michelle Alozie as she got up following a tussle between the two.
Extra time failed to produce a goal before Kelly scored the decisive penalty in the shootout after Nigeria had failed to hit the target with their first two spot-kicks. (NAN)