The strike called by hardline Muslim separatists, saw shops, businesses and government offices closed Monday.
The pope last week quoted a medieval text that criticised some teachings of the Prophet as "evil and inhuman".
He later apologised for offending the Muslim religion.
Malaysia is not satisfied with Pope Benedict XVI's apology.
The Foreign Minister, Syed Hamid Albar, says Muslims have felt oppressed and the apology by the Pope is inadequate to calm Muslim anger.
Syed Hamir says the pope must retract his entire statement, saying the Pope had only stated he was "deeply sorry" about the negative reaction the comments received.
The President of Indonesia, the world's largest Muslim nation, is reportedly hopeful that the Pope's apology will end the global outcry among Muslims.
The Detikcom online news agency quotes Susilo Bambang Yudhoyono, as praising Indonesia's Muslim leaders for calling on people to respond calmly to the Pope's speech last week.
Pope Benedict says the medieval quotes he used on holy war have been misinterpreted.
He says the view that the Prophet Mohammad brought only "evil and inhuman" things to the world does not reflect his personal opinion.
The Pope says he was merely quoting the view of a 14th century Christian emperor, in an effort to stimulate a frank and sincere dialogue on religion with great mutual respect.