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The National Statistics Institute (INE) said on Tuesday that the trade deficit, which is for goods only, rose to 3.547 billion euros ($4.23 billion) in the period.
In November alone, however, exports rose more than imports - by nearly 12 percent versus 10.4 percent, respectively.
In September-November, exports to European Union countries, Portugal's main market, rose by 11.7 percent while imports from those countries increased by 11.2 percent. Exports outside of the European Union rose by just 5.9 percent, while imports from non-EU countries soared by almost 21 percent.
The country has been running a surplus in the combined trade of goods and services, which includes the booming tourism sector, helping the economic growth.