The Times said the hackers appeared to be looking for "the names of people who might have provided information to Mr Barboza," but said there was no evidence that sensitive emails or files from the reporting were compromised.
The paper said that with the help of outside computer experts, it had managed to kick out the intruders and prevent them from breaking into its systems again.
"They could have wreaked havoc on our systems," Times chief information officer Marc Frons said of the hackers. "But that was not what they were after."
The Times said Bloomberg News was also targeted by Chinese hackers, after publishing in June a report on the wealth accumulated by relatives of Xi Jinping. In November, Xi was elevated to leader of the Chinese Communist Party.
The Times asked AT&T, which monitors its computer network, to watch for unusual activity after learning of warnings from Chinese officials that its investigation into the Wen family's wealth would have "consequences."
It also briefed the Federal Bureau of Investigation on the hacking. But with the attacks persisting after the Wen investigation was published, the Times hired IT security firm Mandiant on November 7.