"These first, targeted steps make substantial progress in constraining the creative techniques used to avoid U.S. taxes, both in terms of meaningfully reducing the economic benefits of inversions after the fact, and when possible, stopping them altogether," Lew said. "While comprehensive business tax reform that includes specific anti-inversion provisions is the best way to address the recent surge of inversions, we cannot wait to address this problem."
"While there's no substitute for Congressional action, my Administration will act wherever we can to protect the progress the American people have worked so hard to bring about," Obama said in a statement following the Treasury announcement.
Read MoreCNBC explains: Tax inversions
The Treasury said the actions it took Monday were designed to ensure that tax inversions became economically unfeasible for many companies. Along with the IRS, the Treasury issued a formal notice that the government said would prevent U.S. companies from accessing a foreign subsidiary's earnings while deferring U.S. taxes through what it called "hopscotch" loans.
The notice would also prevent inverted companies from restructuring a foreign subsidiary in order to access the subsidiary's earnings tax-free, the Treasury said.
The move would also block inverted companies from transferring cash or property from what's known as a "controlled foreign corporation" to the new parent company to completely avoid U.S. tax.
Read MoreDemocrats don't want to solve tax-inversion issue
And finally, the Treasury said the notice would make it "more difficult" for U.S. entities to invert by strengthening the requirement that the former owners of the U.S. entity own less than 80 percent of the new combined entity.
The measures, a senior Treasury official said, will take effect for any deal that is not closed by Monday. Lew said currently proposed inversions "will no longer make sense" after the announcement.
Lew emphasized these actions are not attempting to restrict "genuine cross-border mergers."
Read MoreCongress could link inversion plan, tax breaks: Lawmaker
A spokesman for House Speaker John Boehner responded to the announcement, saying that "the answer is to simplify and reform our broken tax code to bring jobs home—and help grow our economy and create even more American jobs."
The White House, through both the Obama and Lew, has contended that American companies conducting inversions are benefiting from the economic and market benefits of their home country, and then leaving without paying their fair share. With a steady stream of speeches on the topic, the administration has been laying the foundation for a new law prohibiting the practice.
But even before that step takes place, Obama has attempted to dissuade companies from inverting, telling CNBC in July that moving tax domiciles out of the U.S. "is neither fair, nor is it something that's going to be good for the country over the long term."