The players were led off the pitch early in the second half after Twente fans, angry at Brazilian Douglas Costa's dismissal late in the first half, chanted insults at referee Ruud Bossen.
Second-placed Twente lost 2-1 after conceding the winner in the fourth minute of stoppage-time, suffering a blow to their title hopes.
Erik Falkenburg won it for Alkmaar after Twente had equalised a minute from time through Luuk de Jong. The hosts also finished with 10 men after Nick Viergever's 63rd minute dismissal.
Twente are three points behind leaders PSV Eindhoven who were held to a 0-0 draw at home by third-placed Ajax Amsterdam.
Dutch under-21 international midfielder Georgino Wijnaldum hit four goals in Feyenoord's 5-1 mauling of fourth-placed Groningen.
Wijnaldum became the first Feyenoord player in 21 years to score four in one match to give the Rotterdam side a lift in a difficult season.
Wijnaldum netted a first-half double and after Nicklas Pedersen had pulled one back just before the break, he converted two second-half penalties. Ron Vlaar added a fifth goal.
Feyenoord moved up to 13th place, six points above the relegation play-off places.
