How do I cap off / remove a single sprinkler head?
It depends on where the sprinkler head is located within that zone.  If the sprinkler head that you are capping is not a dead end on the line, then you can cap it at this sprinkler head.  If it is a dead end, then you need to go to the prior sprinkler head to cap the line. 


  A dead end occurs with the last
  sprinkler in a series. Capping a dead
  end leaves water in the underground
  line with nowhere to go. If the
  sprinklers are spaced far apart, this
  wastes water pressure. In areas prone
  to freezing, it can cause water in the
  line to ice and damage the pipe. Dead
  ends should be capped at the preceding
  or next-to-last sprinkler head.
  Reference: http://www.doityourself.com/stry/how-to-cap-off-a-sprinkler-head


And you do not replace the rotor with a cap but actually just remove the sprinkler head and cap the line.  Removing the sprinkler head is very easy to do.  Just get a trowel and dig down around the sprinkler head until you have enough clearance to unscrew the current sprinkler head without getting soil in the line.  

But before you start the work on capping/removing this sprinkler head, I would try adjusting either the current sprinkler head or the other zones sprinkler head to reduce the amount of water being delivered to that spot.  Depending on the type of sprinkler heads you have, you might be able to replace/adjust one or both of the sprinkler nozzles to reduce the flow.  Or look into adjusting the pattern on the sprinkler to deliver less water in your area.  Or you can even reduce the amount of time that one of these zones is watering.  My point is that someone already did all that work to install the line and sprinkler so try some other steps first.  There have been plenty of times that I have planted a tree or plant or did some other landscaping that blocked a sprinkler heads spray area and then wished I had another head in that location.