The bill reduces the impact of the sequester but will force lawmakers to agree on specific spending cuts.
Former Pentagon General Counsel Jeh Johnson won Senate approval on a 78-16 vote.
Some of the legislative proposals are in conflict with reorganization plans unveiled earlier this month by Defense Secretary Chuck Hagel.
The idea is to create an incentive for agencies to relinquish spectrum as part of a plan to free up 500 megahertz for commercial use by 2020.
The measure targets critical infrastructure protection while providing no new regulatory authority for the Department of Homeland Security.
A coalition of industry groups is asking lawmakers to keep supply-chain restrictions out of upcoming funding bills.
A revised version of the Pentagon policy bill could be considered in the House this week, but IT acquisition reform will have to wait until at least 2014.
The final deal calls for $1 trillion in spending for fiscal 2014, reduces sequestration cuts, adds money for defense and domestic programs, and requires newly hired federal employees to contribute more to their retirement plans.
The HHS secretary is also calling for the creation of a chief risk officer position at the Centers for Medicare and Medicaid Services tasked with reducing risks associated with major policy initiatives.
Open letter urges Congress and the president to ensure U.S. surveillance efforts are "restricted by law, proportionate to the risks, transparent and subject to independent oversight."
A Republican critic claims gaps in the department's defenses "would be obvious to a 13-year-old with a laptop."
Legislation alone will not fix federal IT management, Richard Spires argues, but there are fundamental problems that a new statute can help address.