In a match of few chances in the compact El Madrigal ground it was the former Everton teenager who made all the headlines with a show of petulance midway through the second half.
Rooney was booked in the 64th minute for bringing down Quique Alvarez. It looked an innocuous challenge and Rooney obviously thought so as he ironically clapped in the referee's face and was instantly dismissed by the same official that sent David Beckham off at France '98.
It was another black mark for Rooney following last week's shenanigans in Belfast.
United hung on for the remaining 26 minutes to take a point from an instantly forgettable encounter.
The visitors created the first half-chance in the seventh minute when Paul Scholes' shot was blocked after Cristiano Ronaldo had beaten the offside trap and turned a brilliant cross into the danger area.
In the 18th minute, after Ruud van Nistelrooy had won the corner, Villarreal's Uruguayan goalkeeper Mario Sebastian Viera got across his goal well to keep Mikael Silvestre's powerful header out.
Midway through a tight first period Rooney picked out van Nistelrooy who headed wide but it wouldn't have counted anyway as the Dutchman had strayed offside.
The Yellow Submarines had beaten Everton 4-2 on aggregate in the final qualifying round of the competition to reach this stage but they struggled to reproduce that form in the opening 45 minutes of this encounter.
In the 33rd minute Gabriel Heinze limped out of the action to be replaced by Kieran Richardson and four minutes later Rio Ferdinand did well to get in the way of Juan Pablo Sorin's goalbound effort.
Almost immediately a sweet Villarreal moved ended with Edwin van der Sar making a stunning save to deny Rodolfo Martin Arruabarrena.
Vieira then fumbled Ronaldo's cross straight to van Nistelrooy but Gonzalo Javier Rodriguez made an acrobatic clearance off the line and Ferdinand headed the rebound over the bar.
Six minutes after the break Diego Forlan had a great chance to score against his former club but bent his shot just wide after being set up by the increasingly influential Sorin.
When United hit back Alan Smith headed a corner towards the predatory van Nistelrooy but the striker was unable to turn the ball home from close range. Rooney's shot was then deflected just wide as United began to step up the pace.
The second half was becoming increasingly open but after Rooney's dismissal the game tightened up again.
Sorin mis-hit a shot straight to van der Sar after being set up by Marcos Antonio Senna with 11 minutes left and Ferdinand headed Senna's free-kick on to his own crossbar in stoppage time but both sides seemed content with a point - as they appeared to be from virtually the first whistle.