The Malaysian Maritime Enforcement Agency (MMEA) said the two were rescued by local fishermen.
One of the rescue victims looked weak and was sent to a hospital for further treatment.
However, nine crew members are still missing.
MMEA said the Brunei National Search and Rescue Coordination Committee (NRCC) activated a search-and-rescue (SAR) mission on Wednesday (Aug 7) to track down a fishing boat swept away into Malaysian waters.
The Putrajaya Maritime Rescue Coordination Centre (MRCC) channelled this information to the relevant agencies and requested assistance as well as assets to find the victims.
"The Kota Kinabalu Marine Rescue Sub-Centre (MRSC) was informed that nine victims wearing safety jackets were spotted in Semarang waters on Wednesday.
"The Royal Malaysian Air Force (RMAF) was mobilised to the area to find the victims, but they could not be found," said MMEA in a statement.
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