Goalkeeper Yassine Bounou emerged as Morocco’s hero, producing a decisive save to deny Crysencio Summerville from the spot before Ismael Saibari converted the winning penalty to send the Atlas Lions through.
The victory sets up a last-16 meeting with Canada in Houston on Saturday.
The encounter looked destined to end in Dutch victory after Cody Gakpo broke the deadlock midway through the second half. The Liverpool forward, who recently suffered the loss of his unborn child, celebrated emotionally with teammates after finding the back of the net.
Just as the Netherlands appeared set to progress, Morocco struck deep into stoppage time. Defender Issa Diop rose unmarked to head home a cross from substitute Chemsdine Talbi in the first minute of added time, forcing the contest into extra time.
Morocco had created the clearer opportunities throughout a fiercely contested match that featured several physical challenges and kept Brazilian referee Wilton Sampaio busy.
The Atlas Lions nearly opened the scoring in the 20th minute when Neil El Aynaoui directed an Achraf Hakimi corner toward goal, but Dutch goalkeeper Bart Verbruggen produced an excellent reflex save. Moments later, Verbruggen was again called into action, tipping Hakimi’s powerful effort over the crossbar.
The physical intensity continued, with Saibari fortunate to avoid punishment after catching Jan Paul van Hecke with an elbow during the first half.
Although the Netherlands controlled much of the possession, they struggled to create clear-cut chances. Their best first-half opportunity came just before the break when Micky van de Ven unleashed a powerful long-range effort that Bounou brilliantly pushed over the bar.
Van Hecke, who suffered a head injury during an earlier collision, remained heavily involved and produced a strong tackle on El Aynaoui before halftime.
Morocco also threatened before the interval, with Saibari narrowly missing a dangerous cross that flashed across the face of goal.
The second half produced chances at both ends, but the momentum shifted after Netherlands coach Ronald Koeman introduced Wout Weghorst following the hydration break.
The substitute immediately influenced the game, flicking on a long pass to release Summerville, whose cross found Gakpo diving in to score what seemed the decisive goal.
However, Morocco refused to surrender and found a dramatic equaliser through Diop’s late header to extend the contest.
The Atlas Lions almost completed the turnaround early in extra time when Soufiane Rahimi raced clear on goal, only for Verbruggen to produce another outstanding save to keep the Dutch in the game.
The match was eventually decided from the penalty spot. Despite Neil El Aynaoui missing Morocco’s opening kick by striking the crossbar, Bounou’s crucial save from Summerville gave Saibari the opportunity to seal a memorable victory and send Morocco into the next round.