For every astronomical unit (AU) between the Earth and the craft, ground control loses 4km of tracking accuracy. That means we can only guess a satellite's location orbiting around Pluto, about 50 AU, within a radius of 200km. You're not going to catch an asteroid with that level of inaccuracy.
Instead, Werner Becker and his team at the Max Planck Institute for Radio Astronomy have devised a method for spacecraft to triangulate their own positioning in space based on the relative locations of known pulsars—rapidly spinning neutron stars that emit blasts of high energy radiation in precise intervals. By measuring how long it takes for the emissions of at least three pulsars to reach the craft, compared against their predicted values, the spacecraft should be able to determine its location to within 5 km. This is essentially the same method used by cell towers and the global positioning system, but over massive distances.
There are many technical hurdles that must be overcome before this concept is actually feasible. For one, different pulsars emit radiation at different wavelengths, which can only be received by collecting dishes of a specific size. The 21cm waves that Becker's team is investigating would require an array measuring 150 square meters. This of course leads to the problem of designing and packing a sufficiently large—and, more importantly, sufficiently light—dish into the craft and successfully launching it into space. More here.