Manchester United won their first derby since 2012 after running out convincing 4-2 victors at Old Trafford.
Yaya Toure was heavily criticised post-game, while fellow City midfielders Fernandinho, James Milner, David Silva and Jesus Nevas failed to contain their United counterparts in the centre of the park.
And Rooney said manager Louis van Gaal and United's coaching staff identified City's weakness in midfield.
"We know some City players are not the best at tracking back and defending and tracking runners and we felt we could make them pay for that and we did," Rooney said.
"We have got players who can score goals from midfield and, to be honest, we felt that was going to win us the game and it was proved to be."
Sunday's triumph saw third-placed United move four points clear of City in the Premier League standings with six matches remaining.
However, Rooney was quick to point out that the Manchester club "are still a work in progress".
"It is great how things are going and the performances we are putting in, but it has to continue," the striker said.
"We said earlier in the season that we were working on things and it was going to take time. It is starting to show now with the training we have been putting in. We have been working really hard.
"Each game is different and we have been training for each game in a different way, depending on how the opposition plays. There is no detail left unturned and we have been prepared really well.
"Last season was a tough one for us and we had to overcome that and there was also new players coming in, so we knew it would take time. It is starting to pay off now because we are starting to show what we can do, but we have to continue that to the end of the season and finish as high up as we can and take that into next year."
