The message was sent between the two Koreas' Red Cross organisations who regularly handle official cross-border communications, the south's unification ministry said.
"The North said in the message that it conveys deep condolences that so many passengers, including young students, died or went missing due to the sinking of the ferry Sewol", the ministry said.
Until now, North Korea had been the glaring exception among the messages of sympathy, condolence and support that have poured in from around the world after the Sewol sank with devastating loss of life last Wednesday.
North Korea's state media has barely commented on the tragedy that has dominated global headlines for the past seven days.
The confirmed death toll stood at 150 on Wednesday, but 152 were still unaccounted for, their bodies believed trapped in the inverted, submerged ship.
Heads of state across the political and geographical spectrum have sent personal messages, including US President Barack Obama, Russia's Vladimir Putin and China's Xi Jinping.
Not a word, however, from North Korean leader Kim Jong-Un who, the North's official KCNA news agency reported, had thoroughly "enjoyed" a performance by the popular, all-female Moranbong Band on the evening of 16 April, around the time the full scale of the ferry disaster was emerging.
North and South Korea technically remain in a state of war, as the hostilities of the 1950-53 Korean War were concluded with a ceasefire rather than a formal peace treaty.
Their heavily militarised border remains one of extreme Cold War sensitivity, but declarations of sympathy at times of national grief are not unprecedented.
When North Korean leader Kim Jong-Il, Kim Jong-Un's father died in December 2011, the South Korean government offered its condolences to the North Korean people.