[avar]

The NASA website seems to imply that it's done manually: http://mars.jpl.nasa.gov/msl/mission/rover/brains/

Presumably there's some basic functions in the radio stack they use where they can trigger operations like shutdown, startup, reboot, switch boards etc.

[gsnedders]

NASA normally has pretty low-level stuff. To the point of being able to do full firmware updates — though obviously that's something they don't want to risk ordinarily.