The basket by Arcidiacono gave the Wildcats a two-point lead and pushed them into the finals against Iowa. Kansas will meet Texas-El Paso in the consolation game.
Kansas fought back from a double-digit deficit in the second half and took the lead when Frank Mason completed a 3-point play with 34 seconds remaining.
Arcidiacono, however, hit his huge shot and Mason missed a 3-point try that would have put the Jayhawks back in front.
Two free throws by Villanova's James Bell completed the scoring.
The Wildcats have won all six of their games this year and were led in scoring Friday by Darrun Hilliard and Dylan Ennis with 14 points each.
Mason paced the Jayhawks (5-1) with 12 points.