Corn also edged higher as rain delays to harvesting were also forecast in parts of the US Midwest, though expectations for good yields were curbing corn and soy markets.
Wheat dipped slightly, giving up earlier marginal gains to add to Wednesday's 1.3 percent decline. The cereal remained under pressure from beneficial rains for dry US wheat belts and stiff export competition from Russian wheat.
The Chicago Board of Trade's (CBOT) most-active soybean contract was up 0.4 percent at $9.62-1/4 a bushel by 1134 GMT, extending similar gains the previous day.
Corn rose 0.4 percent to $3.49-3/4 a bushel, while wheat edged 0.2 percent down to $4.41-1/4 a bushel.
"The US soybean harvest is being delayed as rains seem to be an issue," said Phin Ziebell, agribusiness economist at National Australia Bank.
"There are some problems with Brazilian planting, but that is a little bit speculative at this stage."
Brazilian oilseeds industry group Abiove estimated the nation's soybean output at 108.5 million tonnes in the 2017/18 season, down from a record 113.8 million tonnes in the previous crop cycle.
The potential for a La Nina weather pattern in the coming months, which can cause dry conditions in Argentina, has added to uncertainty over the South American growing season.
However, strong expected yields for US soybean and corn crops could keep a lid on prices as the harvest progresses.
"US corn and soybean yields continue to rise as benign end-of-season conditions boost late grain and pod fill," Thomson Reuters Agriculture Research analysts said in a note.
Soybean prices have also been underpinned by brisk demand from China in recent weeks, shipments could be slowed by a Chinese national holiday this week and reports that suppliers a struggling to find high-quality US beans after hurricane damage.
Grain markets will get a fresh indication of export demand from weekly US export sales data at 1230 GMT.
Wheat prices remained capped by export competition created by a record Russian harvest this year, underscored by Egypt's latest purchase of Russian wheat on Tuesday.
Commodity funds were net sellers of CBOT corn, wheat and soymeal futures contracts on Wednesday and net buyers of soybeans and soyoil, traders said. Prices at 1134 GMT.