Kurt DelBene also won praise from his former bosses at Microsoft, including company founder Bill Gates.
"Kurt is a talented and capable executive, with a track record of successfully managing complex large-scale technology projects," Gates said. "Working with Kurt over many years, I know him to be a passionate advocate for using technology to solve difficult problems at scale. He brings deep expertise as a manager and engineer to his new responsibilities. I'm certain he'll make an important positive contribution in his new role with HHS."
(Read more: More Obamacare extensions)
Microsoft CEO Steve Ballmer said "Kurt's a phenomenal leader who established Microsoft Office as a world-class service for billions of people. Clearly, Kurt's technical and business skills will be invaluable in his new endeavor."
When DelBene takes over on Wednesday, he will be facing a less dire situation than the one Zients had to deal with after his appointment in late October.
Nearly two months of widespread software and hardware fixes made by government workers and private contractors during Zients' tenure at HealthCare.gov have left the site functioning much better than it had been after its botched Oct. 1 launch, with quicker load times and a sharply reduced error rate.
But it still needs to process what officials predict will be several millions enrollments in coming months. And the construction of a back-end system that handles critical financial transactions for insurers who sell plans on the site has been repeatedly postponed because of the frantic rush to fix the consumer interface.
Although enrollment on HealthCare.gov has greatly increased after the site was essentially relaunched at the beginning of December a slew of upgrades the pace of sign-ups is believed to still be well below the rate needed to hit 7 million enrollees nationwide by the close of enrollment in March, the target set by Obama officials.
For coverage that would begin Jan. 1, consumers have until next Monday to enroll in insurance bought through either the federal or state-run Obamacare exchanges.
—By CNBC's Dan Mangan, with additional reporting by Eamon Javers. Follow them on Twitter @_DanMangan and @EamonJavers