Between 50 and 100 people attended the service at the university's Loyola campus chapel on Monday morning.
The event was closed to the media, and just one photographer was allowed inside, said Yan Shi, president of Concordia's Chinese Student Association.
"The last 30 days have been the most difficult time in our life," Lin's mother said in a eulogy. "We lived in the agony of grief of losing a loved one and missing him desperately every day."
She described her son as a kind, disciplined, sincere, open minded and mild-tempered.
"You can’t imagine how sad we are! Our hearts are broken and bleeding. Every day we live like walking dead without a soul," a copy of her eulogy in English said.
Lin was killed and dismembered between May 24 and May 25 in a heinous incident that captured headlines around the world.
The Chinese national was studying computer engineering at Concordia and worked at a corner store.
His dismembered torso was recovered in a discarded suitcase in Montreal, while his feet and hands were mailed separately to federal political parties and Vancouver schools after his killing.
Luka Rocco Magnotta, a 28-year-old Toronto-area man, has been charged with first-degree murder and other offences linked to Lin's death.
Magnotta is awaiting trial in Montreal after his high-profile arrest earlier this month in Berlin.
Lin's family travelled from China to Montreal after his death and have kept a low profile since their arrival.
His mother said they hoped to see justice served after their son's death.
She said tears "sprouted from our eyes" any time the family saw a picture of Jun Lin.
"We wept and wept until our tears were exhausted, our voices were choked and we could not get a word out. Our lovely son, poor child, where are you now? Where are you? Your mom and dad miss you. We miss you very much, so much."
Concordia University is handling donations to the Jun Lin Family Fund, set up last week by Concordia's Chinese Student Association.