Kuala Lumpur composite index finished down 0.6 percent at 1,789.07. It rebounded from an intraday low of 1,780.21, backed by better-than-expected economic data.
Malaysia's economy grew a faster-than-expected 5.8 percent in the fourth quarter from a year earlier even as falling oil prices and sluggish global demand hit exports.
Tenaga shares shed 5.3 percent, the worst drop since October 2008, after the government said it cut electricity tariff in Peninsular Malaysia and the Borneo state of Sabah following declines in prices of feedstock and crude oil.
The Philippine index rebounded 0.4 percent after a 0.5 percent loss on Wednesday. The central bank said after market close that it left its benchmark interest rate on hold, as expected, and signalled it can stay on the sidelines for some time.
Stocks in Singapore snapped two days of gains, while Thailand, Indonesia and Vietnam rose marginally amid caution over the ongoing Greek debt negotiations.