Commander Mark Carruthers said the call was received about 6pm but, given the onshore winds, by the time the rescue vessel arrived the 25-year-old man, 17-year-old girl and boat were already ashore near Iluka Beach.
Fremantle Volunteer Sea Rescue was also on its way to help but was stood down.
The boat had capsized when it lost its mast as it passed over a reef.
The pair swam to shore and were helped out of the water by local police.
They suffered minor cuts and bruises and suspected mild hypothermia, and were treated by St John Ambulance before being taken to Joondalup Health Campus.
The vessel was righted on the shore and tied to rocks.
Whitfords VSR has also been involved with the search for missing City Beach woman Robyn Santen.
Mr Carruthers said they received a call from Water Police about 5pm on Sunday and had a vessel on the water from 5.30pm to 10pm and again all Monday morning.
�We covered a fair few kilometres of ocean,� he said.
�We believe she had swum the Rottnest Channel Swim so would be a strong swimmer but we�ve had no confirmation she entered the water.�
Ms Santen was last seen on Saturday evening and her car was found at the City Beach carpark on Sunday.