I would still use a plunger to push down whatever may still be in the pipe. There is a way to find out if your pipe is still clogged without water overflowing the toilet bowl.
You can attempt to flush your toilet without overflowing it by following these steps:
Turn off the inlet valve behind the toilet to cut off the toilet's water source.
Remove half of the water in the toilet's water tank.
Flush the toilet.
This procedure will do two things:
If the toilet is not clogged, it will flush and of course if it is clogged, it will not flush
If it will not flush, then without a water supply, it will not overflow.
If it flushes, then turn the water valve back on and proceed as usual after you clean the toilet.
If it does not flush, then keep the water off and begin plunging again or call a professional to snake the drain.