Mata had no place in Giggs' first XI as United interim boss on Saturday, but scored twice after replacing Danny Welbeck on the hour.
The dominant Old Trafford win rounded off a week of strife for United, following David Moyes' sacking on Tuesday.
A 41st-minute penalty from Wayne Rooney eased any nerves that may have set in after a scrappy first half.
Rooney netted again from distance just three minutes into the second period, setting the stage for Mata to add gloss to the scoreline.
And Giggs hailed the Spaniard's strength of character to put in a top performance when others may have become disheartened.
When quizzed on the decision to drop Mata, Giggs admitted: "That was a tough one, as it was leaving so many players out.
"He was disappointed and I expect that, it would be strange if he wasn't. But he just showed the class that he's got both as a player and as a professional.
"He put on a half-hour masterclass and he was brilliant and I was really happy for him because it's not easy.
"He's got a big price tag and to not start the game was disappointing for him and really pleased that he came on and made such an impact."
