The announcement came after a more than two-hour hearing that was closed to the public.
The judge has not given any explanation for the sealed proceeding, only noting that a transcript of it would become public after Manafort's case concludes.
Prosecutor Greg Andres is telling jurors that the case boils down to greed and deception.
"We've rested because Mr. Manafort and his legal team do not think the government has met its proof", Downing told Reuters.
Closing arguments in the case are scheduled for Wednesday morning. The government reiterated to the judge there were "hundreds" of exhibits the jury could potentially review during deliberation in addition to the testimony of the 27 witnesses called be the government.
Attorney Kevin Downing will likely deliver closing arguments for the defense and argue that Manafort did not intentionally engage in wrongdoing.
Also Tuesday, Ellis rejected a defence motion that the case should be dismissed on those same grounds.
Manafort, 69, is facing tax evasion and bank fraud charges after being accused of hiding income earned from his Ukrainian work from the IRS.
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James Brennan, a vice president at Calk's Chicago bank, Federal Savings, testified in court the bank was aware Manafort had lied about his finances to obtain the loans but proceeded anyway because of Calk.
Prosecutors say Manafort hid money in offshore bank accounts and then used it to pay for over $6 million in NY and Virginia real estate, items such as antique rugs and fancy clothes, including a $15,000 jacket made of ostrich skin.
Calk, who served as an economic adviser to Trump during his presidential campaign, wrote to Manafort after the election with a list of eight administration roles and 19 ambassadorships he would be interested in holding in the new administration.
While several others charged in the investigation, including former Manafort aide Richard Gates, have pleaded guilty and agreed to cooperate in the Mueller probe, Manafort has maintained his innocence.
"The plea deal that [Mueller] gave to Gates is shameful", McCarthy said Tuesday on "Outnumbered".
Gates testified that he helped Manafort commit crimes in an effort to lower his tax bill and fund his lavish lifestyle.
Prosecutors are typically allowed a final rebuttal argument before the judge gives instructions and finally hands the case over for jury of six men and six women to determine Manafort's fate. They'll also introduce some evidence they hadn't presented through witnesses but are allowed to discuss during closings.