The country's second-largest listed bank by assets said on Tuesday net profit fell 47 percent to 90.4 million euros ($115 million), above the 59 million euros expected by analysts.
Net interest income rose almost 4 percent from a year earlier to about 907 million euros, in line with the average forecast.
Provisions for bad loans and asset depreciation climbed 14 percent to 752 million euros, said the bank, which made trading gains of 564 million euros.
Profit numbers last year were flattered by the sale of a stake in Brazilian bank Bradesco for 115 million euros.
The bank said its Core Tier 1 capital ratio at the end of September was 10 percent measured by European Banking Authority criteria and 10.7 percent according to the Bank of Portugal's rules. The central bank's end-2012 requirement for core capital was a ratio of 10 percent.
At the end of last month, BES became the first Portuguese bank to return to the bond market in two years with a 750 million euro 3-year unsecured issue.
Portuguese banks were shut out of the debt and interbank funding market by the sovereign debt crisis in 2010 and have been forced to rely on the European Central Bank for liquidity.
BES said its dependence on ECB funds fell by 3.9 billion euros to a net borrowing position of 9.8 billion euros at the end of September, but the reliance on ECB funds continued to be "fundamental". It held 4.2 billion euros in Portuguese government debt at the end of September.
BES stocks closed 1 percent higher on Tuesday before the results were released, outperforming the broader market in Lisbon, which was almost flat.