There were 127 votes in favour of the agreement, while 84 voted against, according to International Trade and Industry Ministry Mustapa Mohamed.
Mohamed said the Senate was expected to ratify the agreement on Thursday, paving the way for Malaysia's participation in the trade pact.
The US-led trade deal is aimed at spurring trade in the Pacific region.
Signatories include Brunei, Chile, New Zealand, Singapore, Australia, Canada, Malaysia, Japan, Mexico, Peru, the United States and Vietnam.
The deal is expected to be ratified next month in New Zealand.
- DPA