The defending champions started the game strongly trying to break the deadlock, and they had a good shout for a penalty on 14 minutes following a challenge by Joan Capdevilla on Park Ji-Sung but the referee waved away United's protests.
However, with time moving on Villareal gained more possession in midfield as United failed to create any real chances until the end of the first half.
The Spaniards looked even better after the interval and they nearly scored in the 59th minute but Guillermo Franco saw his back heel hit the post from Lopez Angel's cross.
In an attempt to boost his attack, Alex Ferguson brought on Cristiano Ronaldo who was playing for the first time since picking up an injury at EURO 2008.
The Portuguese almost helped United score but his right flank cross was met by Jonny Evans who could only hit the post nine minutes from time.
The Yellow Submarines stood their ground for the rest of the game to earn the draw in Manchester.
In the group's other game, Danish newcomers AaB Aalborg came away with a valuable draw from Celtick at Parkhead.
The Scottish champions saw a 29th minutes penalty missed by Barry Robson as the ball struck Karim Zaza's legs in the Aab goal.
The Danes had to complete the rest of the game with ten men after the referee bizarrely sent off Michael Beauchamp instead of Michael Jakobsen after the latter's professional foul on Giorgios Samaras in the 79th minute.
The two results leave all group E teams level with one point after the group's opening fixtures.