Now substitute x=rcos(phi) and y=rsin(phi) into those expressions.
You will get formulas that are almost the same as what you started with. The difference is due to the following:
The formula you derived answers the following. Given a counter clockwise rotation of the point, what are its new coordinates.
Your original question was this: If we rotate the coordinate axes, what are the new coordinates with respect to the rotated axes. To answer this we have to realize that rotating the coordinate axes counterclockwise is equivalent to rotating the points clockwise. So your new coordinates will be the coordinates you get after rotating your point clockwise. But the formula you derived is valid for counterclockwise rotations. To convert it, you must substitute -theta in place of theta. Then you will get the formula that you first asked about.