Workers had pitched tents on Thursday in anticipation of worshippers filling the main hall on Friday and spilling over outside into Islamabad's monsoon-season heat and humidity.
The protesters say they want the mosque's senior leader, now in detention, returned to his post.
The group chanted slogans against Pervez Musharraf, the president, and called for Ghadi Abdul Aziz to be released.
The mosque had been hastily restored and reopened after it was badly damaged in fighting between students at the neighbouring religious college and government troops.
Its roof has been replaced, and bullet-scarred walls patched and painted in yellow. The rooftop minarets have been recoated in white.
Kamal Hyder, Al Jazeera's correspondent in Islamabad, said students arrived at the mosque armed with red paint and quickly began repainting the mosque its original colour.
The study centre was also badly damaged in the assault and has since been demolished.
Outside the mosque, dozens of police and paramilitary officers remained on patrol, and barbed wire still encircled part of the complex.
The mosque was left scorched by explosions and sprayed with bullets after commandos stormed the complex on July 10 to end a week-long siege by those inside. At least 102 people died in the fighting and violence earlier in the siege.
|The Red Mosque was riddled with bullets [AFP]|
Ul-Haq said that 50 bodies found in the mosque after the siege were still to be identified.
He denied that the government was hiding the exact number of casualties.
After the siege, the government sealed off the central mosque and moved quickly to have it repaired, amid outrage in Pakistan that a sacred place had been the scene of violence.
Ul-Haq said the government will pay for the education and accommodation of students from the demolished study centre if asked for.
A senior municipal official said the school would not be reconstructed.