The data hub behind the Obamacare website went down on Tuesday night and was fully restored on Thursday morning.
For the 14 states and the District of Columbia that operate their own sites, service was restored on Wednesday morning.
But for the 36 states whose exchanges are run by the federal government, service didn't resume until Thursday morning.
At issue was a federal data hub, used by the state sites and the federal site, to verify applicants' income, citizenship and eligibility.
"Verizon Terremark has successfully resolved their issue with the networking component overnight," said Brian Cook a spokesman for the Centers for Medicare and Medicaid Services.
A similar outage had occurred on Sunday.
The latest outage stretched on Wednesday even as Health Secretary Kathleen Sebelius was grilled over broader site issues by members of a House committee.
"Hold me accountable for the debacle," she told them. She called using the site a "miserably frustrating" experience.
Since going live on October 1, major issues with HealthCare.gov have prevented people from registering and applying for coverage.
Sebelius said that by "the end of November, we are committed that the vast majority of users will be able to review their options, shop for plans, enroll in coverage without the problems way too many have been experiencing."
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