Mr Javid said the Labour leader had done a "good job" when he was director of public prosecutions and deserved "absolute respect" for his work in the post.
His comments came after Mr Johnson's long-standing policy chief Munira Mirza dramatically quit on Thursday citing his refusal to withdraw his claim that Sir Keir had failed to prosecute Jimmy Savile for child sex offences.
Chancellor Rishi Sunak also distanced himself from the Prime Minister's attacks, saying he would not have made the comments.
Mr Javid told reporters: "Keir Starmer, when he was running the DPP, did a good job and he should be respected for it, it is a tough job and he deserved absolute respect for that," he told Sky News.
"But the Prime Minister has also come out and clarified those remarks, and that is important."
Asked if the Prime Minister still had his support, Mr Javid said: "Of course he does. Absolutely."
Ms Mirza's departure came on a dramatic day in which three other senior aides announced they were leaving in the wake of Sue Gray's interim report on lockdown parties in Downing Street.
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The resignations continued on Friday, with the Conservative Home website reporting that Elena Narozanski, a special adviser in the No 10 policy unit, was also quitting.
Her departure was later confirmed by the Prime Minister's official spokesman, who said: "I have seen that departure reported. My understanding is that it is correct."
The spokesman said the departures of three other senior aides announced on Thursday had all been agreed before Ms Mirza's shock resignation.
Chief of staff Dan Rosenfield, principal private secretary Martin Reynolds and director of communications Jack Doyle were leaving by mutual consent.
"The departures of those three individuals were agreed with the Prime Minister ahead of Munira's departure yesterday. Those were mutual decisions," the spokesman said.
The moves came after Mr Johnson promised sweeping changes in No 10 in the wake of Ms Gray's highly critical findings about the leadership in Downing Street.
Mr Reynolds organised the notorious "bring your own booze" event in the Downing Street garden, Mr Doyle was reportedly at at least one of the gatherings now under investigation by the police, while Mr Rosenfield has been criticised over the Government's initial response to the reports.
Energy minister Greg Hands said it was the Prime Minister "taking charge" after the battering he had endured over the so-called partygate affair.
"The Prime Minister was absolutely clear on Monday that there would be changes at the top of No 10 and that is what he has delivered," he told Sky News.
"The Sue Gray report update said that there were failings at the top of the operation. This is the Prime Minister taking charge."
In the wake of the resignations, Mr Johnson attempted to rally staff with a line from Disney's The Lion King, telling them: "Change is good."