A New Zealand Defence Force C-130 Hercules aircraft was sent to the location of the beacon and spotted the skipper waving from a life raft.
Maritime NZ senior search and rescue officer Geoff Lunt said van der Mespel has now been safely rescued from his life raft and is aboard the Norfolk Guardian.
He said the rescue vessel had made it to Norfolk Island but the yachtsman and assisting crew were stuck on board due to bad weather.
"I have spoken to police on the island and the weather is still quite bad so there has been suggestion it might be a couple of days before they can offload anyone or any supplies.
"The ship will just wait off the island until suitable conditions allow for any transfer of persons or stores," he said.
Van der Mespel's wife Jenny posted on social media yesterday afternoon to confirm he was safe and doing well.
"Phil is alive and well and aboard Norfolk Guardian, due to land at Norfolk Is this evening," the post read.
"Sadly we have lost Waimanu: her mast came down and punched a hole in the hull and she sank."