The man took his case to the Federal Court to challenge the cancellation of his visa by then-home affairs minister Karen Andrews in December 2021.
He argued Ms Andrews wasn't the relevant minister at the time because Mr Morrison had been sworn into that portfolio six months before her decision was made.
But that argument was rejected on Wednesday by Federal Court Justice John Snaden.
He said it was a matter of notoriety that Mr Morrison and others had been appointed in secret, or at least without public or parliamentary oversight, to various ministries.
Both he and Ben Morton were sworn in as home affairs minister concurrently with Ms Andrews in 2021, he said.
The man argued the same office could be occupied by only one person at a time and as a result Ms Andrews had no authority in the portfolio at the time his partner visa was cancelled by her on character grounds.
But High Court justices have previously said that the appointment of more than one person to a ministry does not go against the Constitution, the judge said.
"There is no constitutional imperative for concluding that the appointments of Mr Morrison or Mr Morton as Minister for Home Affairs brought with it the cessation of Ms Andrews' tenure," Justice Snaden said.
He did not accept that when Ms Andrews made the visa cancellation decision she lacked the authority to do so.
The Afghan man also argued that neither Ms Andrews nor the department secretary knew that Mr Morrison had been appointed to the portfolio.
Justice Snaden found there was no evidence to establish that they didn't know, and there was no proper basis to infer it.
Ms Andrews declined an invitation to concede that neither knew of Mr Morrison's appointment, he said.
Regardless, Justice Snaden said there was no legal requirement that the minister know or even consider whether others held the same powers.
Mr Morrison became the first former prime minister to be censured by parliament over his secret appointments to multiple ministerial portfolios.
A censure motion passed the House of Representatives 86 votes to 50.
Ms Andrews, who had called for Mr Morrison to resign from parliament, abstained from the vote.
