The chancellor said Mr Johnson had given a "perfectly valid explanation" over why he compared women wearing the Muslim niqab to "letterboxes" and "bank robbers" in a newspaper article last year.
Mr Javid, who is of Pakistani Muslim heritage, also denied that the Tory leadership had ever faced accusations of Islamophobia - only hours after the Muslim Council of Britain said the Conservatives had a "blind spot" to anti-Muslim hate.
However Mr Javid repeatedly failed to say whether he would use the same language as the prime minister about Muslim women.
It comes amid a long-running row over allegations of Islamophobia in Tory ranks, heightened by Mr Johnson's refusal to apologise for using inflammatory language in newspaper columns before he became prime minister.
Mr Javid claimed the Tory leadership has never been accused of Islamophobia, despite widespread claims that the prime minister's 2018 article was a prime example.
Speaking at an election event in Bolton, he said: "Whenever this issue has come about the Conservative Party, no-one has ever credibly suggested that it's an issue with the leadership of the party, whether that's the leader of the party of the day or the chancellor or other senior figures.
"No-one suggested that. And that is one of the big differences I think in what we're seeing with the Labour Party today."
Asked about the prime minister's remarks, Mr Javid said: "The prime minister has been asked that question a number of times publicly and people have the right to ask him what they wish.
"And he's explained why he's used that language. In the case of the article you're referring to it was to defend that rights of women, whether Muslim women or others to wear what they like, so he's explained that and I think he's given a perfectly valid explanation."
But Mr Javid told The Independent during the Tory leadership contest: "I think they're wrong. I don't think any serious politician should use language like that."
The MCB, which represents 500 mosques, educational and charitable groups, said the Tories have approached the issue of Islamophobia with "denial, dismissal and deceit", accusing the party of tolerating it in its ranks and allowing it to "fester in society".
A spokesperson said: "As a faith community, we commonly are threatened by Islamophobia. This an issue that is particularly acute in the Conservative Party who have approached Islamophobia with denial, dismissal and deceit.
"It is abundantly clear to many Muslims that the Conservative Party tolerate Islamophobia, allow it to fester in society, and fail to put in place the measures necessary to root out this type of racism.
"It is as if the Conservative Party has a blind spot for this type of racism."
Mr Johnson told reporters on the campaign trail that he did not agree with the claim that his party has approached Islamophobia with "denial, dismissal and deceit".
"What we do in the Tory party is when anybody is guilty of any kind of prejudice or discrimination against another group then they're out first bounce," he said.
Mr Johnson said his party would hold an inquiry into "all forms of prejudice" - despite having previously pledged to hold one specifically on Islamophobia.
The row came as the MCB offers its support to the Jewish community after the Chief Rabbi Ephraim Mirvis warned that British Jews were "gripped with anxiety" about the prospect of a Jeremy Corbyn-led government.
Mr Corbyn failed to address the comments directly at a speech to launch the party's race and faith manifesto, but he insisted that Labour did not tolerate antisemitism "in any form whatsoever".
The Labour leader insisted anti-Jewish racism was "vile and wrong" and that the party had a "rapid and effective system" for dealing with complaints.