The best way to handle this is to first turn off the water to the toilet and then flush it to drain the tank. If you have a plunger, place it on the bottom of the bowl and plunge up and down to try to dislodge the clog.
First, make sure to turn off the water to the toilet. Then, flush the toilet several times in order to empty out as much water as possible. Next, if you have one, use a plunger to try to push the clog down.