Real had wanted to receive their title on a stage in the centre of the Santiago Bernabeu, but the former Spain international sat defiantly in his seat in the standsReal Madrid with the Liga trophy after Sunday's 4-1 victory over Mallorca.
According to AS, Real had intended to lift the cup on a specially constructed stage in the middle of the field but the former Athletic Bilbao midfielder remained in the stand.
Consequently, Villar, who was whistled by the Madrid crowd, presented the title to Iker Casillas and Sergio Ramos in front of the Bernabeu's royal box.
The sight of Casillas and Ramos raising the trophy together was significant as it was the first time that two captains had been put forward to receive the cup.
It was therefore the final piece of history in a record-breaking season for Madrid, whose victory over Mallorca saw them become the first side to reach the 100-point mark in a single campaign.