The bill signed Friday has long been campaigned for by health advocates but is opposed by the tobacco industry.
It requires companies to devote about half the space on packets to warnings including photographs of internal organs ravaged by smoking.
The Philippines has long had a conflicted attitude towards smoking, with the government trying to discourage it even as it encourages a politically powerful tobacco-growing industry.
In 2013 Aquino signed a "sin tax" bill dramatically raising the taxes on tobacco products.
The Philippines is the latest developing country to follow Western nations in requiring shock pictorial health warnings.
A similar Indonesian law came into force in late June, but was initially widely ignored.
A 2009 survey revealed that 28 percent of adult Filipinos are smokers.