Acting Police Commissioner Stephen Brown said it was fortunate the plane didn't hit the gathered people.
"For reasons yet unknown, it's entered the waterway, thankfully without injuring anyone else on the ground or any other people who are here at the event," he said.
Police have confirmed a man and a woman were on board when the crash happened near Heirisson Island.
The pilot and passenger were confirmed dead a short time later. It is reported that the pair are a husband and wife.
Police said they would wait until morning to remove the plane.
At the South Perth foreshore, families setting up for the Skyworks rushed to the river's edge as the plane crashed into the water.
"I was watching the show and all I saw was the plane just nose dive into the water," witness Natasha Eyles said.
"As it hit the water you could see the plane break into two."
Witness Craig Newill was with his family when the plane went down.
"We were so stunned and shocked," he said.
"We could see him stall.
"His wings were pointing to the sky and to the water and we thought 'this is not good' then we saw it break into two pieces."
PerthNow reader Kristijana Dutkovic said: "Saw it do a couple of passes over the water and then it dropped straight into the water.
"Boats were quick to respond though - hope they [are] alright."
The City of Perth confirmed just after 6pm that Skyworks had been cancelled because of the tragedy.
The display, which attracts massive crowds each year, had been due to start at 8pm. It is the first time the event has been cancelled in its 33-year history.
