The Indonesian index was the worst performer in the region, slipping 0.8%, with all major sectors in the red on broad-based selling.
Indonesia's Rupiah firmed against the dollar on Wednesday, "which implies that the move lower in equities in Jakarta is part of a general Asian pull-back," said Jeffrey Halley, market analyst at OANDA.
In Singapore, the benchmark index fell 0.6%, extending losses to a second consecutive session. Consumer services and utility stocks largely underpinned losses.
Philippine stocks extended losses and closed nearly 0.5% lower after the government said the economy's contraction this year could be greater than earlier predicted.
At odds with the regional trend, Malaysian stocks jumped 1.3% to their highest level in nearly two weeks as the economic growth in the first quarter beat expectations. However, it will likely contract in April-June.