The 31-year-old's failure to start at Wembley is the latest disappointment for Rooney, who has been marginalised by both United and England.
Amid reports of a possible move to the lucrative Chinese Super League, Rooney issued a statement this week insisting his future lies at Old Trafford, at least until the end of the season.
Rooney had hoped for a place in the starting line-up at Wembley after United playmaker Henrikh Mkhitaryan was ruled out with an injury suffered in the midweek Europa League clash with Saint Etienne.
But United manager Jose Mourinho opted for Juan Mata, Jesse Lingard and Anthony Martial as the attacking support for central striker Zlatan Ibrahimovic.
Mata was included after flying back to England on Saturday evening following his grandfather's funeral in Spain.
United, bidding for the first major silverware of Mourinho's reign, were captained by Chris Smalling in Rooney's absence, while world-record signing Paul Pogba started in midfield.
Southampton manager Claude Puel selected Italy forward Manolo Gabbiadini to lead the attack in place of Shane Long, whose semi-final second-leg goal at Liverpool booked his team's place in the final.
Uruguay defender Martin Caceres was on the bench as he awaited his debut after his recent move to Southampton.