Exports totaled $47.49 billion, up 0.4 percent from the same month of last year, and imports fell 2 percent to $44.14 billion.
It was the 14th straight month of a trade surplus.
The government credited the higher exports in March to increased shipments to Asian markets, including China.
"Exports increased slightly on growing shipments of IT products and shipments to newly emerging markets," it said in a news release.
The increase was achieved despite an 18 percent drop in exports to Japan and a 15.4 fall in those to the United States.
Yonhap quoted an official as saying that the decrease in shipments to Japan might have been partly due to the decline in the Japanese yen against the South Korean won.
"First, the drop in exports to the U.S. appears to have been caused largely by a base effect as shipments to the U.S. in March 2012 surged 27.9 percent year-on-year to $5.9 billion," said Lee Woon-ho, director general for trade.
"But partly, the weaker Japanese yen appears to have also affected the drop."
South Korea's exports in the first three months of the year amounted to $135.5 billion, up 0.5 percent from the first quarter of last year, while imports dipped 3 percent year-on-year to $129.7 billion.