The opposition motion was defeated by 357 votes to 262.
Labour has claimed the Greensill affair marks the return of “Tory sleaze” at the heart of government.
The row erupted after it emerged the former Tory prime minister David Cameron had lobbied the chancellor Rishi Sunak, including by text, to include Greensill in the government’s Covid-19 loan scheme.
Boris Johnson has faced criticism after it emerged that an inquiry he ordered into the scandal would be led by top lawyer Nigel Boardman, a non-executive director at the business department.
In a new twist it emerged just hours before today’s Commons vote that Mr Boardman is by the government paid for the part-time role.
In response, Mr Johnson’s spokesman said he would not act as a director while the inquiry was carried out and was not being paid “from now onwards”.
However, the revelation will fuel questions about his independence.
Mr Boardman, the son of a former Tory Cabinet minister, had already come under fire after it emerged his law firm previously campaigned against limited curbs to lobbying rules.
Earlier Mr Johnson rejected Labour’s call for a wider inquiry into the lobbying scandal, claiming “it won’t do a blind bit of good”.
But he was forced to admit that he did not recall the last time he spoke to Mr Cameron.
He told MPs: “The honest truth is… I cannot remember when I last spoke to Dave”
However, he insisted they had not discussed the Greensill affair.
Mr Johnson did admit that it was unclear that the "boundaries" that are supposed to exist between Whitehall and business had been "properly understood".
Yesterday it emerged that a former head of procurement in Whitehall became an adviser to Greensill Capital while still working as a civil servant, a move that was approved by the Cabinet Office.
At Prime Minister’s Questions, Mr Johnson said he shared the "widespread concern about some of the stuff that we’re reading at the moment".
"I do think it is a good idea in principle that top civil servants should be able to engage with business and should have experience of the private sector," Mr Johnson said.
"When I look at the accounts I’m reading to date, it’s not clear that those boundaries had been properly understood and I’ve asked for a proper independent review of the arrangements that we have to be conducted by Nigel Boardman, and he will be reporting in June."
As she set out Labour’s proposals for a parliamentary inquiry, Labour’s Rachel Reeves described the probe ordered by Mr Johnson as “wholly inadequate” and “an insult to us all”.
She also accused Mr Cameron of a “cynical and shabby” decision to break his silence on the scandal last weekend during a period of “national grief” following the death of the Duke of Edinburgh.
Cabinet Office minister Julia Lopez defended Mr Boardman’s appointment, saying: "I have no doubt that any recommendations from his work on Greensill will not only be unsparing but they will lead to meaningful change should it be necessary."