Summit host Saudi Arabia has led Arab efforts to isolate Syria diplomatically and has also backed calls for the Syrian rebel opposition to be armed, which Foreign Minister Saud al-Fasial described in February as "an excellent idea".
But speaking to reporters after the summit, OIC Secretary General Ekmeleddin Ihsanoglu said he "did not see much support for external military intervention" in Syria during the summit.
He described the decision to suspend Syrian membership as "a message to the international community ... that the Islamic community stands with a politically peaceful solution and does not want any more bloodshed".
The 57-member body's rebuke is mostly symbolic, but it shows Syria's isolation - as well as that of its ally Iran - across much of the Sunni-majority Islamic world.
The summit, which has taken place late on consecutive nights because of the Ramadan fast, had been billed as a diplomatic showdown between Sunni Saudi Arabia and Shi'ite Iran, which have backed different sides in sectarian conflicts in the region.
Iranian Foreign Minister Ali Akbar Salehi criticised Syria's suspension as he left Mecca early on Thursday, saying it was contrary to the organisation's charter.
"Before taking this decision it is necessary to invite the Syrian government to the meeting so that it can defend itself and so that participants can listen to its official views," the official news agency, IRNA, reported him as saying.
Saudi King Abdullah tried to conciliate Iran at the summit opening by placing President Mahmoud Ahmadinejad at his side to welcome Muslim leaders in a gesture Saudi political analysts said was aimed at putting old grievances aside in the quest for a resolution to the Syrian crisis.
He also suggested founding a centre for dialogue between Islam's sects, another move aimed at trying to defuse some of the region's sectarian tensions. That proposal was adopted by the summit.