The peaceful protest, involving various activist groups and opposition parties, featured scores of people wearing anti-TPP T-shirts and holding placards warning against the mammoth trade deal.
While a few hundred gathered near Independence Square, around 3,000 others, mainly supporters of the opposition Pan-Malaysian Islamic Party, marched to a nearby field to listen to speeches given by critics of the agreement.
Prominent Malaysian opposition figure Chua Tian Chang, better known as Tian Chua, told the crowd that the TPP will affect Malaysia's sovereignty and that "jobs will be reduced and prices of medicines will go up".
"This will only help the rich people. It will not help the poor people in Malaysia and I don't see any benefits for my family and I," said Mohammad Noor Ismail, a student who attended the protest, The Bangkok Post reported.
The TPP aims to create the world's biggest free-trade area including Canada, Brunei, Chile, Malaysia, Mexico, New Zealand, Peru, Singapore, Vietnam, the United States, Japan and Australia.
Both China and the United States are pushing their own free trade visions for the economically vibrant and populous region.
Thailand and Indonesia are considering joining the TPP, but they say they also remain committed to the Regional Comprehensive Economic Partnership (RCEP), a 16-member group that includes the 10 Asean states plus China, India, Japan, South Korea, Australia and New Zealand.
China is pointedly excluded from the TPP, part of Washington's attempt to ramp up influence in the region with its "pivot" to Asia.
The TPP will be formally signed in New Zealand next month, officials in Wellington said on Thursday. Following the signing, each country has two years to complete the ratification process before the accord takes effect.
Critics in the countries involved have vowed to fight ratification, saying it threatens labour rights and environmental protection.
The Malaysian parliament is expected to debate next week whether the country should sign the accord which involves significant market openings from Canada, the United States and Japan, and establishes mechanisms to handle disputes between foreign investors and governments.
Malaysian opponents of the trade deal have criticised the secrecy of the talks and warned that the TPP could saddle consumers with higher medicine costs and provides too much protection for foreign companies.
US President Barack Obama has described the deal as a foundation for "21st century trade".