Gonzalo Higuain and Kaka both netted braces but it was Ronaldo who caused all the damage with arguably his best display of the season to help Madrid bounce back from their poor showing in Lyon and trim the gap to Primera Division leaders Barcelona back to two points.
Ronaldo scored a brilliant free-kick opener, which he dedicated to the victims of the disaster that has struck his home island of Madeira, and also created goals for Higuain, Kaka and Xabi Alonso as Madrid made it 12 wins out of 12 at the Bernabeu this season.
Marcos Senna and Nilmar pulled goals back for Villarreal but they could not live with Madrid, whose coach Pellegrini will have been especially pleased with the win over his former club as his position has been called into question in the wake of the Lyon defeat.
After a quiet opening, Madrid took control with two set-piece goals in as many minutes.
Ronaldo was the man to break the deadlock in the 18th minute with a magnificent free-kick, sending an unstoppable diagonal shot across Diego Lopez and into the far top corner.
That was the Portugal international's 12th goal in only 14 league appearance, and his celebration included a tribute to Madeira, which has been hit by flash floods that have left at least 40 people dead.
Villarreal were still coming to terms with that thunderbolt when they conceded a second from the penalty spot.
Higuain's heels were clipped by Ivan Marcano as he tried to get on the end of Marcelo's low cross, and referee Cesar Muniz Fernandez immediately pointed to the spot.
The Madrid fans were angry Marcano only got a yellow card for his foul, but they were soon celebrating as Kaka sent Lopez the wrong with the resulting penalty.
Ronaldo missed a chance to make it 3-0 soon after when he side-footed wide from the edge of the box but at that point it did not look like being a costly miss, with Madrid dominating.
However, the mood in the Bernabeu changed in the 30th minute when Senna produced some dead-ball magic of his own to bring Villarreal right back into the game.
That was tough on a Madrid side that had had little to worry about up to then but the hosts responded well and should really have extended their lead, with Ronaldo testing Lopez and Esteban Granero and Kaka both skying decent openings.
Ronaldo also brought another superb save out of former Madrid goalkeeper Lopez just before the break, moments after Iker Casillas had produced similar heroics to keep out Nilmar's deflected cross.
Madrid will have been disappointed not to have been further ahead at the interval but they had to wait only nine minutes of the second half to extend their lead with what was a simple, yet clinical, move.
Alvaro Arbeloa's ball down the right touchline put Ronaldo away and his first-time cross was slotted home by Higuain in the middle.
Ronaldo then set up further good chances for Marcelo and Higuain, but both were missed, before the £80million man was denied one on one by Lopez as Madrid threatened to run riot.
As they did in the first half, though, Villarreal pulled a goal back against the run of play in the 67th minute.
A good move involving Nilmar, Robert Pires and Javi Venta was finished off by the former.
That was only a brief setback for Madrid, though, and they made it 4-2 three minutes later through Higuain.
Ronaldo's pass put Marcelo through on the left and his low cross was slotted home by Higuain.
Ronaldo, almost inevitably, also created the fifth and sixth Madrid goals, slipping in Brazilian ace Kaka to side-foot past Lopez and then winning the penalty that allowed Alonso to seal a comprehensive win with a twice-taken spot-kick late on.
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