Abdulahi Hassan Afrah said the two of the men had both a hand and a foot cut off and a third had only a foot cut off after the Islamic court in the southern port city of Kismayo realized he was already disabled.
He said a crowd of around 400 people, mainly women and children, watched the sentence carried out Friday on the three screaming young men.
"It was most painful thing I have ever seen," he said.
A spokesmen for the al-Shabab militia, Sheik Hassan Yaqub Ali, said the three had admitted robbing passengers on board a truck heading to Kismayo.
None of the three were allowed to appeal the sentence or had access to a lawyer.
The Islamic courts were originally set up to try to counter the bloody chaos of Somalia's 18-year-old civil war. Initially their harsh judgments were welcomed by many of the war-weary population and in 2006 the courts formed the basis for an Islamist administration that controlled much of the capital and southern Somalia.
But the Islamist government was toppled in December 2006 by Ethiopian troops supporting the weak U.N.-backed government, and the Islamists launched a bloody insurgency. The courts are still active in areas under Islamist control, including many neighborhoods in the capital.
In 2008, the courts in Kismayo ordered a 13-year-old gang rape victim to be stoned to death.
But amputations and public floggings are more common.