Friday night's result sees Plymouth move above Luton on the Championship table in 13th place.
Rami Al Hajj had Plymouth ahead before Ibrahim Cissoko struck twice. Victor Moses scored a first goal for Luton since his return to England this month.
Rooney said afterwards: "I thought it was a good performance for different reasons.
"I thought first half we were good at times, controlled the tempo of the game and Luton tried to press us, and I think when we showed composure and played through the press we caused them problems.
"Second half we were a little bit sloppy with the ball and gave it away in dangerous areas at times, but I thought defensively our back four, and in particular the two centre-backs, were excellent.
"Luton are very good at set-pieces and I thought we were brilliant defending them and showed great character and desire to go and head the ball, and then the attacking players get all the praise when they score the goals."