United went ahead with a Rooney header after three minutes but West Brom equalised when James Morrison stroked in a superb shot from the edge of the box after 14.
West Brom blew their chance to secure a first win over United since 1984 when Peter Odemwingie sent a 62nd-minute penalty horribly wide and they paid dearly for it when Javier Hernandez came off the bench to head home a Rooney corner 13 minutes later.
The win takes United to 41 points, three clear of Manchester City, who are at home to Blackpool later on Saturday