What is the correct material to reseal a shower pan to a drain pipe?
it was installed wrong, there's no real correct way to fix this other than starting again and using the correct fitting.

The correct way is to use the pipe fitting that matches the shower base,
you may be able to do from below or it may require disassebling the 
shower floor and walls in addition to cuttihg a hole in ceiling of the room below.

Next best is probably to weld the pipe to the shower base if the two are made of compatible plastics, this could be a fusion weld done with a heat gun with a plastic welding head or (it it's all PVC) a solvent weld done with that Marley stuff.

if you want to make another doomed attempt at sealing it with caulk choose a product that has low shrinkage (preferably no shrinkage)