I have Tata Indigo GLX petrol of MPFI engine,model year 2003,from last few days when my car is on 4th and 5th gear and specially when the ac is on it jerks and also when it jumps on the potholes it shakes terribly,I need solution to this problem as soon as possible.

Sounds like something is loose or wore out. Maybe the rear end, universal joint, tie rods,.

Motor mounts?

Is this a physical shaking with an enigne that's firing well or is it an engine misfiring that's causing the shaking?

Yea, where is the shaking originating. The things I suggested would be more underneath, smoothy's would be more front end.

Does it jerk or does it shake? Jerk sounds like drive train, while shake sounds like suspension or motor mount as smoothy suggested. Or does it do both?
Does the A/C function properly? Possibly the A/C is putting extraordinary load on the engine due to failed bearing or other component as jerking in higher gear usually indicates not enough engine power being delivered (for that particular gear ratio), and under normal conditions downshifting should stop the jerking. What happens when you shift to a lower gear when jerking occurs?