"There is no change to our longstanding policy on cross-Strait issues," he said Friday.
China's Foreign Minister Wang Yi initially called the call a "little trick played by Taiwan."
The ministry later issued a formal statement on the conversation, saying it had lodged "a solemn representation to the United States" over the call.
"It must be pointed out that there is only one China in the world, and Taiwan is an inalienable part of China," the statement added. "One China policy is the political basis of China-U.S. relations."
The call is believed to be one of the first between a U.S. president and a leader from Taiwan in decades. China, a regional powerhouse, has long resented U.S. military presence in the Asia-Pacific region, and has rebuffed U.S. pressure to curb its activity in the disputed South China Sea.
While the U.S. does not formally recognize Taiwan as an independent nation, it has sold $12 billion in arms to the island as part of a 1970s agreement that commits Washington to helping Taiwan defend itself.