The midfielder created space with a wonderful first touch from Pennant's ball and evaded Bramble's challenge on the edge of the box before firing past the onrushing Kirkland.
Wigan pressed forward but the closest they came to another equaliser was when Titus Bramble's hopeful long-range lob sailed over the top of Green's crossbar.
Dimitar Berbatov had claims for a penalty turned down after going down under Titus Bramble's challenge, Rooney forced Chris Kirkland to tip round the post from 25 yards, Nemanja Vidic had an effort cleared off the line by Paul Sharner, and Rooney - again - curled onto the far post after dancing round Maynor Figueroa on the byline.