That was the highest toll in an attack since Lebanon's 1975-1990 civil war.
Coming a week after a bombing in the Beirut bastion of Shiite party Hezbollah, a close ally of Bashar al-Assad, the bombings risk further exacerbating tensions between supporters and foes of the Syrian president.
"There are at least 29 dead and 500 wounded, many of whom are in serious condition with burns and with head wounds," said Georges Kettaneh, director of the Lebanese Red Cross.
An AFP reporter saw a number of charred bodies near the Al-Taqwa mosque, in the port area, and the bodies of five children brought out from it.
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As huge clouds of black smoke billowed into the air, television channels aired footage of the dead, of buildings with their fronts blown in and vehicles ablaze.
People rushed to help the wounded, as others hysterically sought their loved ones.
The powerful Shiite movement, whose militia have been fighting for months alongside Assad's troops, linked the Tripoli attacks to the one in Beirut on August 15, which killed 22 people and injured more than 300.
It said they were part of a plan to "plunge Lebanon into chaos and destruction".
Former premier Saad Hariri, a Sunni and Hezbollah opponent, said the "authors of dissension do not want Lebanon to live in peace for one minute; they want the killing machine to mow down the lives of innocents across Lebanon".
The second struck near the port of the restive city with a Sunni majority, close to the home of former police chief Ashraf Rifi, a security source said.
On Wednesday, army chief General Jean Kahwaji said his forces were fighting a "total war" against terrorism whose aim is "to provoke sectarian strife" in the country.
The army had been pursuing a "terrorist cell that prepares car bombs and sends them to residential neighbourhoods," he said.
A Lebanese and two Palestinians suspected of preparing a car bomb attack were arrested days after the latest blast in Beirut, the General Security agency said.