"We face the greatest challenges to our security in a generation," Stoltenberg wrote as he outlined NATO's strengths, amid concerns over the president-elect's position on the US-led alliance.
"This is no time to question the partnership between Europe and the United States."
Trump caused alarm during his election campaign when he suggested Washington would think twice about coming to the aid of an endangered NATO ally if it had not paid its dues, casting doubt on the alliance's core collective defence commitment.
More than 1,000 European soldiers serving in Afghanistan "paid the ultimate price" in an operation that was "a direct response" to the attacks, he added.
He said NATO had made possible the "integration of Europe" and ended the Cold War, adding: "European leaders have always understood that going it alone is not an option."
The alliance continues to play a key role in fighting terrorism and has responded in recent years to "a more assertive Russia", Stoltenberg added.
The US currently accounts for 70 percent of NATO spending.
"It is all too easy to take the freedoms, security and prosperity we enjoy for granted," he concluded.
"In these uncertain times we need strong American leadership, and we need Europeans to shoulder their fair share of the burden.
"But above all we need to recognise the value of the partnership between Europe and America. It remains indispensable.
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