Napolitano said that even though Tsarnaev's name was misspelled, redundancies in the system allowed his departure to be captured by US authorities in January 2012. But she said that by the time he came back six months later, an FBI alert on him had expired and so his re-entry was not noted.
"The system pinged when he was leaving the United States. By the time he returned all investigations had been closed," Napolitano said.
The Russia trip is now seen as potentially important to determining how and when Tamerlan Tsarnaev, the older Boston bomber who died in a firefight with police, apparently became radicalised, and whether he had ties to others.
Tamerlan Tsarnaev was investigated by the FBI at Russia's request and his name was included in a federal government travel-screening database after that, law enforcement officials have told The Associated Press. One official told the AP that by the time of the flight Tsarnaev would have faced no additional scrutiny because the FBI had by that time found no information connecting him to terrorism.
The testimony came during the third Senate Judiciary Committee hearing on sweeping immigration legislation. As at the previous two hearings, the proceedings were overshadowed by the events in Boston.
Ms Napolitano also defended the security procedures that occur when someone applies for asylum to the US, as the Tsarnaev family did about a decade ago. She described an extensive process with multiple screenings.
She said any asylum applicant is thoroughly interviewed and vetted, run through databases, fingerprinted and vetted again when they become eligible for a green card and ultimately citizenship.
Ms Napolitano also said the process has improved in recent years. And she said the new immigration bill would build on that.
