The apartment raid turned up an ISIS flag, a Kalashnikov rifle and ammunition.
But two people escaped after an intense, prolonged firefight, according to a spokesman for the Belgian federal prosecutor's office.
During the raid Tuesday, authorities killed suspect Belkhaid Mohammed, 35. The Algerian had not been on authorities' radar before, spokesman Eric Van der Sypt said in a statement.
A sniper for the Belgian special forces killed Mohammed when he tried to open fire on police from a window.
His body was found next to a rifle and a book on Salafism, a puritanical branch of Islam that dictates only the followers of the Prophet Mohammed practice the correct Islam.
Authorities also discovered 11 loaded Kalashnikov magazines "and innumerable shell casings," but no explosives, according to Van der Sypt.
An intense manhunt followed Tuesday's operation in the southern Brussels neighborhood of Forest. Authorities connected it to the investigation of the Paris terror attacks
that killed 130 people in November.
The raid Tuesday started when four Belgian and two French police officers arrived at what they thought was an empty residence in Forest, according to a senior Belgian counterterrorism official.
"From the moment that the door of the flat was opened, at least two persons ... opened fire toward them," Van der Sypt said.
Three officers -- including a Frenchwoman -- were hurt in the initial exchange of gunfire before managing "to retreat safely," he said. A fourth officer from Belgium suffered a slight injury to the head in a later exchange.
Reinforcements arrived, with bullets flying back and forth for several hours.
There's no change in Belgium's threat level, now at its second highest. But Prime Minister Charles Michel acknowledged the raid underscored the need to be on guard.
"The terrorist threat level is maintained at level three as yesterday's events confirm the threat is still real," he said.
Belgium a focus
It's unclear what connection Tuesday's raid has to the November 13 carnage
in Paris. Belgium has long been a focal point for investigators.
Two terrorist operatives phoned in orders from Brussels
to those directly involved in the Paris attacks, according to a senior Belgian counterterrorism official.
These two had an even more integral role than Abdelhamid Abaaoud, the man long identified as the ringleader of the attacks, according to the official.
Yet others with Belgian connections and ties to the November attacks remain at large.
They include Salah Abdeslam, a Belgian-born French national who lived and spent time with Abaaoud in a Belgian prison. The trail for Abdeslam, one of the few alleged Paris attackers to escape alive, went cold in December, according to a senior European counterterrorism official.
French sources close to the investigation said Abdeslam was not the target of Tuesday's raid.
Many of those tied to the Paris massacre lived in Belgium, and they're believed to have met there before planning attacks.