A forgettable game ended in a drab 0-0 stalemate as Luke Shaw came closest to settling the contest when his first-half effort was turned onto the post.
The dull encounter flared up in the closing stages as West Ham skipper Mark Noble clashed with Paul Pogba - the pair arguably lucky to only walk away with yellow cards.
Mourinho made wholesale changes following Friday's 1-0 defeat at Brighton, his side showing eight alterations as Marcus Rashford and Anthony Martial were two to drop out of the side.
Alexis Sanchez returned to lead the line but could not inspire the Red Devils to victory - although a share of the spoils was enough to ensure they will finish second to runaway champions Manchester City.
"Any team that goes to this kind match where you need something to get some objective, you fight for that,' the manager told reporters.
"The best way to fight for the point was to try to win the match and be safe, which was what we tried.
"But when the game goes to 70, 75 minutes, you don't win, you don't lose, you do the job. You get the point.
"We deserved a point, we deserved second position. When it is not possible to be champions, second position is the best available which was what we got."