Mr Yousaf, who was promoted to the role in June, hit out as legal action to prevent the eviction of asylum seekers got under way.
Housing and homeless charity Shelter Scotland is taking action after accommodation provider Serco issued notices to say it planned to change the locks in cases where asylum applications have been refused and tenants have not moved on.
While Serco announced on Saturday it will pause the rolling programme of lock changes ahead of the court case, Mr Yousaf said this would only provide “temporary relief” for those at risk of losing their home.
First Minister Nicola Sturgeon has already spoken out against the proposals and Mr Yousaf, MSP for Glasgow Pollok, said he was “very concerned” about Serco’s actions.
He said: “I welcome, of course, that Serco have announced a recent halting, but that is just a temporary relief undoubtedly for aslum seekers.
“I would echo the First Minister that some much-needed humanity has to be injected into the system.
“The Home Office immigration and asylum policy has rightly been criticised for being too cruel, for not seeing human beings, for not understanding the reasons why people leave their homes, whether it is war, poverty or conflict.
“There are some real big hurdles in the asylum process, but there is a complete and utter lack of humanity in the system from the UK Government, and that has to change.”
As well as legal action, Serco’s plans have sparked protests in Glasgow, a city which has become home to many of those seeking refuge.
While Mr Yousaf said he could not comment on the legal proceedings, the Justice Secretary added: “Legality aside, there is clearly a desire from the people of Glasgow that they want and are happy for asylum seekers to make Glasgow their home and for refugees to make Glasgow their home.
“That is why we call on the Home Office to take a much more humane approach to government.
“The UK Government could change the legislation around this, if they don’t want to do that we’ve often said as the Scottish Government they should hand the powers over immigration and asylum to the Scottish Government.”
He spoke out after the head of Serco said he did not know how many people housed by the firm in Glasgow would be evicted.
However, chief executive Rupert Soames said it was not true lock change notices would be issued to 330 people.
Speaking on BBC Radio Scotland’s Good Morning Scotland programme, he said: “That is the total number of people we are paying for whom Home Office support has ceased.
“About of third of them have had positive decisions and will be waiting for a month or six weeks or eight weeks to find alternative arrangements and go on and make their lives with legal right to remain, and nobody is going to want to make them homeless.”
Questioned on the figures regarding who would be given lock change notices, he said: “We don’t know, because a number of them, hopefully, will move on.
“We have been looking after, at our expense, people for over two years.
“There are 80 people who have had negative decisions, who are meant to leave the country who we still pay the rent, rate, heating, light for.”
Serco has made an £80 million loss on the asylum accommodation contract in the past five years, Mr Soames said.
The firm has welcomed the legal action as an opportunity to gain clarity from the courts, although it insisted its approach was “fully within the law”.