Trump named Sessions' chief of staff, Matthew Whitaker, as acting attorney general, saying he would soon nominate a permanent replacement for review by the Senate.
As Sessions' deputy, Rod Rosenstein has been the authority over Mueller's probe, but multiple media outlets are reporting that he has officially been removed from oversight of the investigation.
But it's not typical for chiefs of staff to replace the head of an agency when that head resigns, as former CIA staffer and NBC contributor Ned Price pointed out.
"Under Acting Attorney General Matthew Whitaker, it is imperative that the important work of the Justice Department continues, and that the Mueller investigation proceeds to its conclusion unimpeded", he said on Twitter. Rosenstein was at the center of a recent controversy after it was reported that in the spring of 2017 he raised the idea of Cabinet members invoking the 25th amendment to remove the president and suggested that he should secretly record Trump.
Trump told associates that he felt that Whitaker would be "loyal" and would not have recused himself from the Russian Federation probe as Sessions had done, according to two Republicans close to the White House not authorized to speak publicly about private conversations.
Trump was only a few weeks into his presidency in March 2017 when Sessions upset him by stepping aside from overseeing an Federal Bureau of Investigation probe of potential collusion between the Trump campaign and Moscow, citing news reports of previously undisclosed meetings he had with Russia's ambassador to Washington for his recusal.
He also ran for Iowa Senate unsuccessfully.
Some Democrats also considered Sessions too eager to do Trump's bidding and overly receptive to his grievances.
"Mueller has come up to a red line in the Russian Federation 2016 election-meddling investigation that he is dangerously close to crossing", Whitaker wrote in an op-ed a year ago before he came to work for the government.
"In my time as attorney general, we have restored and upheld the rule of law - a glorious tradition that each of us has a responsibility to safeguard", Mr Sessions added in his resignation letter.
Asked whether Whitaker would take control of the Russian Federation probe, Justice Department spokeswoman Sarah Isgur Flores said, "The acting attorney general is in charge of all matters under the purview of the Department of Justice".
As a result of Tuesday's midterm elections, the Republicans lost that control because although they kept the Senate, the Democratic Party seized the House of Representatives. Trump belittled Sessions but, perhaps following the advice of aides, held off on firing him. "He has no reason to recuse himself", Malcolm told VOA.
Now Whitaker is in charge of the Justice Department and Rosenstein reports to him, putting Whitaker in a position to constrain the special counsel if he wishes or if he's directed to do so by the president.
Sessions endured most of the name-calling in silence, though he did issue two public statements defending the department, including one in which he said he would serve "with integrity and honor" for as long as he was in the job.
A copy of Attorney General Jeff Sessions' resignation letter is photographed in Washington on an image of the exterior of the Justice Department.
The Democrats, who won the House in the mid-terms, have vowed to protect it.
"Americans must have answers immediately as to the reasoning behind" Trump's move to remove Sessions, he said.