The attack, the latest in a string of killings, comes exactly one week after a US air strike killed the chief of the Al-Qaeda-linked Shebab rebels, prompting threats of retaliation from the extremists.
"The car packed with explosives hit one of the armoured trucks... 12 civilians in a minibus were killed, and 27 others were wounded," local governor Adukadir Mohamed Sidi told AFP.
The attack took place near the town of Afgoye, some 30 kilometres northwest from the capital Mogadishu.
Witnesses reported a huge blast and wave of fire, with civilians on the busy highway between the town and the capital caught up in the explosion.
"I saw two minibuses with pools of blood, many civilians were killed," said Ali Muhidin, a witness. "The explosion was enormous."
Somalia's government on Saturday warned of a wave of retaliatory attacks by the Shebab following the killing of their commander Ahmed Abdi Godane.
On Friday the Pentagon confirmed that Godane, the leader of Al-Qaeda's main affiliate in Africa, perished in an attack in which US drones and manned aircraft rained Hellfire missiles and laser-guided bombs on a gathering of Shebab commanders.
AU forces are targeting Shebab on several fronts, with Ugandan troops leading the offensives against the main port of Barawe, south of Mogadishu.
The 22,000 AMISOM force, with soldiers drawn from six nations, have been fighting alongside government troops against the Al-Qaeda-linked Shebab insurgents since 2007.
The Shebab have appointed a new commander, named Ahmad Umar Abu Ubaidah.
