Dier had started 19 of Spurs' 21 league games before the Portuguese coach named the England international centre-back on the bench for the match against the Baggies.
The defensive partnership of Toby Alderweireld and Davinson Sanchez helped Spurs to their first clean sheet in seven matches as the North Londoners snapped a run of three straight defeats.
And Mourinho revealed Dier had suffered a loss of confidence after being one of a number of players to make individual mistakes during Tottenham's recent run of sketchy form.
"Players have moments," Mourinho said. "They can be very good, they can be strong personalities, they can be experienced, they can cope with a mistake but in the end, they are men. And they feel more than anyone else these little moments of confidence, of crisis.