Werfel, 42, replaces acting commissioner Steven Miller, who resigned Wednesday amid the controversy over disclosures the tax agency singled out conservative groups applying for tax-exempt status for extra scrutiny.
It was unclear whether Werfel would be nominated to fill the full-time IRS vacancy.
Werfel, controller at OMB, will guide the agency through the end of the fiscal year, a White House statement said.
He holds a masters degree in public policy from Duke University, a juris doctor from the University of North Carolina at Chapel Hill, and a bachelors degree from Cornell University and served on the Federal Accounting Standards Advisory Board from 2006 to 2009.
"Throughout his career working in both Democratic and Republican administrations, Danny has proven an effective leader who serves with professionalism, integrity and skill," Obama said. "The American people deserve to have the upmost confidence and trust in their government, and as we work to get to the bottom of what happened and restore confidence in the IRS, Danny has the experience and management ability necessary to lead the agency at this important time."