Hundreds of Pakistani policemen set up new checkpoints and cordoned off the area around the compound with barbed wire.
“The mosque will now remain closed for an indefinite period,” Interior Ministry spokesman Javid Cheema said.
Security in Islamabad was also strengthened to thwart possible attacks by Islamist radicals.
Police was deployed at all entry and exit points of the capital and the nearby city of Rawalpindi, where security forces were put on high alert.
The authorities had carried out reconstructive surgery of the head of the suspected suicide attacker to make his face recognizable, while other parts of his body were sent to the laboratory for DNA testing.
The bombing targeted a group of policemen deployed near the Red Mosque to quell an irate mob of some 2,000 Islamic theology students who occupied the compound for several hours after it reopened for Friday prayers.
The police used tear gas to disperse the crowd and arrested around 100 rioters as it regained the control of the Lal Masjid mosque compound.