The court ruled that the nine men, most Belgian nationals of Moroccan origin, were members of a Belgian cell of the Moroccan Islamic Combat Group (GICM), linked to al-Qaeda.
The GICM has been accused of involvement in the March 2004 train bombings in Madrid, which killed 191 people and injured around 1,900.
The cell has also been blamed for attacks in Casablanca in May 2003 in which 45 people were killed.
The court found three of the men guilty of leading the cell. It sentenced Abdelaker Hakimi and Lahoussine El Haski to seven years in prison and Mustapha Lounani to a six-year term.
Of the other accused, three were jailed for five years, one for four years and one for three years. The last was given a four-month suspended sentence.
Two other men were found guilty of illegal residency but the court did not sentence them. A further two were acquitted.
Most of the 13 men on trial, who all denied the charges, are Belgian
nationals of Moroccan origin.
The presiding judge, Pierre Hendrickx, described the nine found guilty as "extremely dangerous".
The trial, which began in Brussels three months ago, is the first to be covered by Belgium's tough new anti-terror laws. These laws allow for sentences of up to 15 years.
The court said the nine accused had provided support to the GICM.
Some were notably found to have housed GICM members after the March 11, 2004, train bombings in Madrid and to have raised funds for the group.
The prosecutors did not establish during the trial that the men had planned or carried out any attack.
The 13 suspects were picked up in two separate operations, the first in March 2004 at Maaseik on the Belgian-Dutch border, the second in swoops in Brussels and Antwerp in June that year.
Some of the accused are also thought to be linked to the Netherlands-based Islamist group "Hofstad". One of Hofstad's members, Mohammed Bouyeri, has been given a life sentence for murdering Dutch film-maker Theo van Gogh.
The trial in Belgium was the latest in a series in the country involving suspected Islamist militants.
In June 2004, a 10-year jail term was handed down to former Tunisian footballer Nizar Trabelsi forfor planning a suicide attacks on a Belgian NATO base on behalf of al-Qaeda leader Osama bin Laden.
During the same trial, other militants were convicted of running a forged documents ring to help send would-be volunteers to engage in Islamic Jihad in Afghanistan and Pakistan.
The killers of Afghan resistance leader Ahmad Shah Masood on September 9, 2001, are thought to have benefitted from the scheme. They blew Mr Masood and themselves up with a booby-trapped television camera two days before the September 11, 2001, attacks on the United States.
In October 2004, a Brussels criminal court sentenced five Islamist radicals to five years in jail in a trial that shed light on links between militants and what the judge described as "youth deprived of moral bearings".
Belgium beefed up its legal arsenal to combat extremists in September 2005 by making it easier to wire-tap and carry out unannounced police visits to suspects.