The CBO's economic projections were finished before the partial government shutdown, but it estimated that as a result of the shutdown, real GDP was 0.1 percent lower in the fourth quarter of 2018, and it will be lower in the first quarter of 2019 by 0.2 percent or $8 billion.
A federal worker stands with a placard reading "Will Work For Pay" as other federal employees stage a rally to call for a vote on the shutdown on Capitol Hill in Washington, Jan. 23, 2019.
The $3 billion reflects a hit of 0.1 percent to economic activity during the fourth quarter of 2018 - an amount that will be permanently lost.
"Some of those private-sector entities will never recoup that lost income", it added.
In the wake of the report's release, Senate Minority Leader Chuck Schumer called for an end to President Donald Trump's shutdowns.
The CBO said the cost of the shutdown will make the USA economy 0.02 percent smaller than expected in 2019.
The President's shutdown inflicted needless pain and chaos in the lives of millions of Americans, and stole billions of dollars from the economy.
"Government is open again, but we can not forget what shutdowns mean: unnecessary anguish for millions of Americans", said Rep. Madeleine Dean of Pennsylvania in a tweet.
A new government report says that the US budget deficit is set to hit $897 billion this year and predicts that economic growth will slow as the effects of President Donald Trump's tax cut on business investment begin to drop off. About 800,000 federal workers didn't receive paychecks for five weeks, and federal contractors won't receive any at all.
Some shutdown costs, however, are harder to quantify, the office said. "To put it on a sustainable one, lawmakers will have to make significant changes to tax policy and spending policies - making revenues larger than they would be under current law, making spending for large benefit programs smaller than it would be under current law, or adopting some combination of those approaches".
The CBO said its assessment of the effects of the 35-day shutdown on the US economy, the world's largest, showed that $3 billion in economic activity was lost in the waning days of 2018 after the government closures took effect December 22, and another $8 billion in January, extending to last Friday when the shutdown was ended.
According to the CBO the shutdown hurt economic growth because it affected roughly 800,000 workers and delayed federal spending on goods and services.