In parliament, Trudeau called on all Canadians to "stand up against xenophobic and anti-Semitic attitudes that still exist in our communities, in our schools, and in our places of work".
"There is little doubt that our silence permitted the Nazis to come up with their own final solution".
"[Hitler] watched as we refused their visas, ignored their letters and denied them entry", the Prime Minister told the House of Commons.
In May 1939, the St. Louis left Germany with passengers who included more than 900 Jewish German citizens seeking sanctuary.
Cuba and the United States had rejected the 907 German Jews aboard the MS St. Louis, a German ship, before they attempted to land in Canada in 1939. The passengers were forced to return to Europe and more than 250 later died in the Holocaust. From 1933 to 1945, only about 5,000 Jewish refugees were accepted because of Canada's discriminatory "none is too many" immigration policy.
"To harbour such hatred and indifference towards the refugees was to share in the moral responsibility for their deaths", Mr. Trudeau said.
"We also apologize to others who paid the price of our inaction who we doomed to the ultimate horror of the death camps", he added.
Jewish Canadians "are understandably feeling vulnerable" and there have been calls "to protect synagogues and other places that are at risk of hate-motivated crimes", Trudeau said during his parliamentary address.
Mr. Trudeau also warned of an "alarming rate" of discrimination and violence against Jewish people today.
"Holocaust deniers still exist. Jewish institutions and neighbourhoods are still being vandalized with swastikas", he said.
Trudeau said Holocaust deniers still exist and anti-Semitism remains prevalent in Canada - the latest numbers from Statistics Canada show Jews are the most frequent target of religiously motivated hate crimes - and North America, shadowed by the shooting deaths of 11 worshippers inside a Pittsburgh synagogue nearly two weeks ago.
The prevalence of anti-Semitism in contemporary society showed itself nearly two weeks ago when a gunman killed 11 worshippers inside a Pittsburgh synagogue simply because they were Jewish, Trudeau said.
The head of Friends of Simon Wiesenthal Center, Avi Benlolo, said it is up to governments to "take serious measures that help counter hate crimes against minority groups". Of those Canada did let in, some 7,000 Jews were held as prisoners of war and jailed alongside Germans captured on battlefields, he said.
The Prime Minister said the "long overdue" apology to the passengers of the St. Louis can not erase the pain suffered by these refugees or those murdered in the Holocaust or their descendants.
"But today, Canadians pledge, now and forever: never again".