Having returned from a double leg break in the summer, the 21-year-old has endured a frustrating comeback campaign.
Shaw has had some issues to overcome this term and s truggled for game time, although the England international had managed to force his way back into Mourinho's plans in recent weeks.
However, the United boss has confirmed Sunday's start against Swansea was his 19th and final appearance of a difficult campaign, having been forced off after just nine minutes.
Press Association Sport understands the left-back was due to see a specialist after scans showed ligament damage in his left foot, which Mourinho says will bring his campaign to a premature end.
"Luke Shaw is injured and it is an important injury obviously," Mourinho said ahead of the Europa League semi-final first leg at Celta Vigo.
Read the full article on eurosport.co.uk: Shaw will not play again this season, Mourinho confirms