Shaun Haywood, 29, faces further felony counts of aggravated mayhem and assault with a deadly weapon, according to Los Angeles County District Attorney Jackie Lacey.
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Haywood allegedly broke into the Australian model's ranch on October 14 in an effort to deliver a letter.
When confronted by a security guard, the defendant is said to have grabbed the guard's knife and slashed his face, prosecutors said. The guard then shot Haywood.
Both the intruder and the security guard were flown to hospital and were left with serious but non-life-threatening injuries.
Haywood denied all three charges at an arraignment hearing on Tuesday, where bail was set at $1.1 million pending a second hearing scheduled for November 7.
If convicted, he faces a maximum sentence of life in state prison.
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Kerr, 33, married Hollywood star Orlando Bloom in 2010 and gave birth to the couple's child the following year.
However, three years later, Bloom and Kerr announced that they were separating and she is now engaged to Snapchat's co-founder, Evan Spiegel.
Kerr, a former Victoria's Secret star who is among the world's highest paid models, was not at home at the time, according to LA County sheriff's deputies.
Australian media reported, however, that she "no longer feels safe in the house" and is planning to return to Sydney.
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