Carlo Ancelotti's side are a point ahead of Catalan minnows Girona, who host Alaves on Monday and will be looking to reclaim pole position.
Spain's top scorer Bellingham broke the deadlock for Madrid with his 13th league goal before Rodrygo Goes doubled their lead.
Villarreal pulled one back through Jose Luis Morales, but Brahim Diaz scored a superb solo goal to restore Madrid's advantage.
Luka Modric drove home the fourth as Madrid fans celebrated a sizeable victory in their final home match of the year.
The only negative news for Ancelotti came in the form of an injury to defender David Alaba, who he replaced in the first half.
The Italian coach put his faith in England international Bellingham to take an attacking role this season for Madrid and it is paying off in virtually every match.
The 20-year-old netted his 17th goal across all competitions in his 20th match this season to get the party started after Madrid saw rivals Barcelona, third, held at Valencia on Saturday.
Madrid, playing at the renovated Santiago Bernabeu with the new roof closed for just the second time, made the early running against Villarreal.
They got their reward midway through the first half when Bellingham leaped high to nod home Modric's delicious clipped cross.
Alaba went off with an apparent knee injury sustained as he challenged Gerard Moreno, who later went off hurt himself along with teammate Alex Baena and Madrid's Ferland Mendy.
With Thibaut Courtois, Vinicius Junior, Eder Militao, Eduardo Camavinga and others out already, Ancelotti's pack is worryingly thin.
However, they did not let it show on Sunday, with Rodrygo doubling the lead from close range after the ball bounced to him in the box.
Early in the second half, Villarreal pulled one back, with Morales finishing past Andriy Lunin, selected over Kepa Arrizabalaga.
But Diaz whisked the visitors' hope away when he turned brilliantly away from Aissa Mandi in midfield, drove forward, swerved Jorge Cuenca and finished with ease.
After Modric added the fourth, Madrid fans brought out the 'ole' chants as their team passed the ball around an increasingly frustrated Villarreal.
Madrid midfielder Aurelien Tchouameni made his return from injury as a substitute in the final stages to round off a largely satisfying night for Los Blancos.
