He then opted to play an unambitious 4-6-0 formation at Old Trafford, with four attacking midfielders given free roles in front of the more disciplined Frank Lampard and Ramires.
To say it didn't work would be an understatement.
Following the match, Mourinho told BBC Sport that transfer target Rooney must make a quick decision about his future in Manchester. He said:
One way or another he has to say 'I want to leave' or 'I want to stay'.
The person that started the story has to finish the story. For the good of everyone, it is time to finish the story.
If you look at a manager like me, a club like us and the people who work at the club with me, we are not silly enough to try to get a player from a big club that doesn't want to sell.
United have already rejected two bids from Chelsea this summer, and with a week left of the transfer window, time is running out for a deal to be done.
When questioned about how long he was prepared to wait for Rooney in the same interview, Mourinho answered: "Twenty-four hours, 48 hours."
The Special One's frustrations regarding the lack of movement are understandable, particularly considering he first made an offer for the wantaway striker back in mid-July.
But Mourinho will be all too aware that during Monday night's showdown the England man showed glimpses of the qualities that make him top of Chelsea's summer wish list.
After coming off the bench to set up two goals in United's season opener at Swansea, Rooney was given a free role from the start behind Robin van Persie.
David Moyes had no issue starting his former Everton player against a side still interested in his services, and the recently appointed boss was not left disappointed.
Rooney put in a performance full of energy and desire, with some neat passing and movement thrown in as well. The only thing lacking was a goal.
The 27-year-old linked up well with his teammates, worked hard to help the United defence and always looked like the Red Devils' most likely goalscorer, particularly when his ambitious 30-yard drive tested Petr Cech.
With Torres struggling for form, Lukaku untested at the highest level and Ba linked with a move away per Ben Jefferson of The Express, Mourinho is desperate for a proven striker to lead the line ahead of a wonderfully creative midfield including Eden Hazard, Oscar and new signing Willian.
Now with a decade of Premier League experience behind him and success in the Champions League under his belt, Rooney fits the bill perfectly for Chelsea as they look to steal United's crown.
Capable of playing as a lone forward, as one of a front two or just off a single striker, Rooney's versatility and all-action style is sure to have appealed to a manager who stressed the importance of mobility in a pre-match television interview, via James Olley of The Independent.
And with just a point and a disappointing attacking display to reflect on after the visit to Old Trafford, Mourinho should be even more determined to land his No. 1 target.
After all, if Rooney had been wearing blue instead of red on Monday, Mourinho's second spell in West London may well have continued with victory against a side sure to be one of their closest title rivals.