BEIJING—U.S. President-elect Donald Trump’s Friday telephone call with Taiwan’s president is plunging U.S.-China relations into uncertainty, potentially jeopardizing crucial cooperation on a range of issues, perhaps most ominously North Korea.

The Chinese lodged an official protest with the U.S. on Saturday, though Beijing focused blame on Taiwanese President Tsai Ing-wen and is likely to show restraint toward Mr. Trump in its initial public responses to the phone call, which breached decades of U.S. diplomatic protocol. Still,...