A bomb-sniffing dog detected the device at Virra Mall in the affluent Greenhills district, local police chief Eduardo Lorenzo said.
"The area is safe now and the bomb, which was rigged to an improvised electronic device, has been defused," he said.
Authorities have been on heightened alert for possible terrorist threats following a spate of bomb attacks in Manila and in Mindanao that killed more than 20 people last October.