The Manchester City forward was felled in the opening minute, but after consulting the video-technology a free-kick was instead awarded, before Anouk Dekker and Lineth Beerensteyn scored either side of Christine Sinclair to send the Dutch through as group winners.
It was the Canadians’ first defeat of the tournament, though Beckie had a chance to rescue a point late on, only to mistime her jump as she tried to head home Adriana Leon’s centre.
The Canucks’ place in the last 16 was guaranteed prior to kick-off, but this defeat in Reims consigned them to a second-placed finish in Group E, meaning they will play either the United States or Sweden in the next round.
Just 58 seconds had passed when Beckie raced onto Sinclair’s flick-on, muscling her way past Desiree van Lunteren, who sent her tumbling to the floor.
Referee Stéphanie Frappart pointed to the spot for what would have been the fastest awarded penalty of the tournament so far, but it was delayed as the boos rang out from the Dutch fans.
That soon turned to cheers as Frappart instead awarded a free-kick, judging the foul to have taken place outside the area after watching it back through VAR.
Beckie was looking lively and saw a fierce drive blocked, but it was her opponents who enjoyed the better chances in a goalless first-half.
Shanice van de Sanden was a constant threat down the Dutch right flank and hit the bar with a drilled cross before teeing up Vivianne Miedama, whose sharp turn and shot was denied by the woodwork.
Within nine minutes of the restart the Netherlands had their breakthrough.
Anouk Dekker stole a yard on the imposing Kadeisha Buchanan to glance Sherida Spitse’s left-wing free-kick into the far corner, but Beckie was involved as Canada levelled on the hour mark.
She played a neat one-two with Sinclair before the ball was worked wide to Ashley Lawrence, who delivered a teasing centre and Canada’s record goal scorer duly obliged from close range.
A draw wouldn’t have been enough for Beckie’s side to clinch top spot, but Beerensteyn made sure the Dutch qualified with a 100% record when she tapped home an inviting cross from van Lunteren 15 minutes from time.