The memorial, organised by Kirk's conservative youth advocacy organisation Turning Point USA, drew tens of thousands of mourners dressed in red, white and blue who filled State Farm Stadium in Glendale, Arizona.
Trump said the 31-year-old was targeted because he stood "for freedom and justice, for God, country, for reason and common sense."
"The violence comes largely from the left," the president said without citing any evidence, in a speech that downplayed political violence from the right and often turned starkly partisan.
"He was assassinated because he lived bravely, he lived boldly and he argued brilliantly.
"He's a martyr now for America's freedom. I know I speak for everyone here today when I say that none of us will ever forget Charlie. And neither now will history."
Kirk was shot dead at an event at a university in the state of Utah on September 10. The alleged perpetrator, a 22-year-old man, was arrested and charged with murder. He faces the death penalty.
Kirk's widow, Erika, paid tribute to her late husband in a more than 20-minute speech forgiving his alleged killer.
"That man, that young man, I forgive him. I forgive him because it was what Christ did and is what Charlie would do," she said.
"My husband Charlie wanted to save young men, just like the one who took his life," she added tearfully, as the crowd applauded solemnly.
In stark contrast, Trump said unlike Erika Kirk, he does not wish his opponents well, saying: "I hate my opponents. And I don't want the best for them.
"I'm sorry. I'm sorry Erika."
At the end of his speech, Trump embraced Erika Kirk, who rested her head against his chest several times as they held hands.
The memorial, organised by Kirk's conservative youth advocacy organisation Turning Point USA, had the feel of a religious revival mixed with a "Make America Great Again" political rally.
Stephen Miller, the powerful White House adviser, vowed to use Kirk's death as a galvanising force to finish the work he began.
"We will carry Charlie and Erika in our heart every single day, and fight that much harder because of what you did to us," Miller said.Â
"You have no idea the dragon you have awakened. You have no idea how determined we will be to save this civilisation, to save the West, to save the republic."
Christian rock music blared through loudspeakers and pictures of Kirk were set on easels throughout the walkways of State Farm Stadium in Glendale, Arizona. The arena, which normally has a capacity of 63,000, appeared completely full. Crowds of people, many wearing MAGA merchandise, had arrived before dawn to secure seats inside the stadium, where they encountered metal detectors amid tight security.
The memorial service included Vice President JD Vance, Secretary of State Marco Rubio and Secretary of Defence Pete Hegseth and young conservatives shaped by Kirk's political influence.
Kirk's death has raised fears about the growing frequency of US political violence across the ideological spectrum, while also deepening partisan divides.
During her remarks, Tulsi Gabbard, the US director of national intelligence, tied Kirk's killing to what she described as a historical pattern in which "political fanatics" eventually turn to violence to defend their ideals.
"They kill and terrorise their opponents, hoping to silence them," she said.
"But in this evil that we have experienced - that Charlie faced - their flawed ideology is exposed, because by trying to silence Charlie, his voice is now louder than ever."
with DPA
