The air zone covers a group of disputed islands controlled by Japan
China monitored the flight of two US bombers that flew across its newly-declared "air defence identification zone", its defence ministry said.
The B-52 planes flew over disputed islands in the East China Sea on Tuesday without announcing themselves, defying new Chinese air defence rules.
Japan and the US are strongly opposed to the air zone declared by China.
They have accused China of unilaterally attempting to alter the status quo and escalate regional tensions.
The new air zone, announced by China on Saturday, overlaps with an air zone set out by Japan and covers disputed islands that are controlled by Japan.
The islands, known as Senkaku in Japan and Diaoyu in China, have been a source of severe tension between the two nations for months.
Japan says China's new zone is "invalid" and has asked its airlines not to provide flight information to the Chinese.
Both the ANA and JAL airlines had initially complied with the Chinese request for their flight plans but said late on Tuesday they would stop doing so.
They had not encountered problems passing through the zone, they said.
'Manage and control'
The unarmed US aircraft took off from Guam on a flight that was part of a regular exercise in the area, US officials said.
A Pentagon official said the US had followed "normal procedures" during the bombers' flight and had not filed flight plans with China.
China says aircraft passing through the zone must obey its rules, including identifying themselves, or face "emergency defensive measures".
However, Wednesday's defence ministry statement after the US flight made no reference to any emergency measures.
"China's air force monitored the entire course [of the US bombers], identified them in a timely way, and ascertained the type of US aircraft," the statement said.
"China will identify all aircraft activity in East China Sea Air Defence Identification Zone", it added. "China has the ability to effectively manage and control the relevant air zone."
The US flight is being seen as a clear signal that the US will not recognise Chinese control over its newly-declared zone, correspondents say.
The flight will also reassure America's allies in the region - Japan in particular - that Washington will stand by its security commitments, reports the BBC's Martin Patience from Beijing.
But, says our correspondent, the big fear is that a misstep on the part of one of the parties could trigger a crisis.
The tensions came amid other military developments in the region.
On Wednesday, Japan's parliament enacted a bill to establish a national security council, giving the prime minister greater control over defence issues.
Meanwhile, the Chinese navy's Liaoning aircraft carrier set out for a mission in the South China Sea - where China is engaged in territorial disputes with other nations - in what China described as part of the carrier's "scheduled training".
The flight of the US bombers triggered anger among Chinese social media users, with widespread calls for a stronger response from Beijing.
Sina Weibo user Han Qingzi wrote: "The US bomber aircraft provocatively barged into China's air defence zone and flew over China's territorial sea - why did the Chinese side not send fighter jets to intercept or accompany the planes? Has there been a dereliction of duty?"
Microblog user Seeking Treasure in Fire said that China should have sent up fighter planes when it was challenged by the US.
"Whether as a warning, or to coerce the US, at least China needs to display some attitude, otherwise, the air defence zone exists in name only, and becomes the world's laughing stock," they said.
However, one Sina Weibo user appeared to point to domestic politics as a motive. "The air defence zone was issued for our own compatriots in China. Our comrades from outside of China need not be so nervous," they said.