The peaceful protest, involving various NGOs and opposition parties, saw scores of people wearing anti-TPP t-shirts and holding placards warning against the mammoth trade deal.
While a few hundred gathered near the capital's Independence Square, around 3,000 others, mainly supporters of 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."
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.
In October, 12 Pacific nations finally reached an agreement on the pact, a major diplomatic coup for Washington.
Both China and the US are pushing their own free trade visions for the economically vibrant and populous region.
The trade deal will be formally signed in New Zealand next month, officials in Wellington said Thursday.
Following the signing, each country has two years to complete the ratification process before the trade accord takes effect.
Critics in the countries involved have vowed to fight ratification, saying it threatens labour rights and environmental protection.
The Malaysian government is widely expected to sign and ratify the deal according to reports.
In October, it had hailed the Pacific Rim trade deal as a boost for commerce, saying it won key concessions in areas including its controversial system of business preferences for its ethnic Malay majority.