Thousands offered the prayers with Saeed, who carries a USD 10 million bounty on his head. Posters with Saeed's photo were pasted in several locations in the city ahead of the gathering.
In his tweet Saeed said, "Time is near when those oppressed in Kashmir, Palestine and Burma will celebrate 'Eid' in the air of Freedom - Insha'Allah. #EidMubarak."
"So, we say Eid Mubarak to you in these testing times; soon world will say Eid Mubarak to you after your triumph. May ALLAH accept."
"ALLAH will not waste your Sacrifices, Ummah will be glorified, Islam will be strengthened, that time is very near #kashmir," he tweeted from his account '@HafizSaeedJUD'.
India has repeatedly asked Pakistan to bring Saeed to justice for masterminding the 2008 Mumbai attacks.
He has often been seen addressing anti-India rallies in Pakistan.
Meanwhile Islamabad says it has no proof against him.
A total of 166 people, including six Americans, were killed in the LeT terror attack in India's financial hub of Mumbai in November 2008.