Several residents saw the men's 6m boat flip after it was hit by a large wave near the sand bar at the mouth, and contacted emergency services shortly after 8am.
The Otago Regional Rescue Helicopter, police search and rescue and an inflatable dinghy from the Brighton Surf Life Saving Club were sent to the area, Constable Don Peat, of Mosgiel, said.
However, both men had been helped from the water by local people and were on the beach when emergency services arrived.
"The men were experienced boaties and have seen first-hand the value of their lifejackets."
The men, believed to be in their 40s, were treated for hypothermia.
One was taken to Dunedin Hospital by helicopter and the other by ambulance.
Both men were released from hospital yesterday.
The men's boat was safely anchored off the sand bar and would be salvaged as soon as possible, Const Peat said.
