Winds from the storm on Friday night blew off the protective covers over the pitch and exposed it to driving rain. Umpires and team captains inspected the pitch late on Saturday morning and called the game off over safety concerns, confirming the match with the Prime Minister's XI would end in a draw.
The first Test begins next Thursday in Perth with later matches scheduled for Melbourne and Sydney.
Pakistan's bowling contingent will be completely different for the first Test, with Shaheen Shah Afridi, Hasan Ali and Mohammad Wasim set to be named after resting for the Canberra match.
The early end to the Canberra match denied Matt Renshaw a chance to build on his unbeaten 136 and press his case to Australian selectors to replace David Warner as an opener when Warner retires.