Hours after governor Arnold Schwarzenegger rejected a clemency appeal and cited Beardslee's "grisly and senseless killings", the warden at San Quentin State Prison north of San Francisco gave the midnight order to proceed.
Beardslee, 61, had spent 20 years on death row since being sentenced to death in 1984 for killing two young women.
California, the nation's most populous state, has the largest death row population in the United States and perhaps the world, but it rarely administers the ultimate punishment.
Lengthy appeals typically last two decades before an inmate is executed.
Five guards strapped a passive Beardslee to a table to administer lethal doses of three chemicals, including potassium chloride, which causes cardiac arrest.
The guards, working in a small room with five windows built as a gas chamber, took about 15 minutes to insert intravenous tubes into each arm. Once the drugs started flowing Beardslee let out a big yawn, blinked his eyes several times and moved his head before his breathing stopped shortly thereafter.
Schwarzenegger says Beardslee's
judgment was not impaired
He spent his last day with his legal team and a female spiritual adviser, prisoner officials said, and did not prepare a final statement. He carried his personal Bible to a waiting area before entering the death chamber.
Earlier, Beardslee declined the state's offer of a special last meal of his choice, a prison official said. So he was offered the same meal as other inmates of chilli, macaroni, mixed vegetables, salad and cake - which he declined. He did ask for grapefruit juice, a prison spokesman said.
After several minutes in which Beardslee was motionless, a note was passed through a hole in the death chamber and the prisoner was pronounced dead at 12:29am (0829 GMT) on Wednesday.
Four relatives of the victims attended the execution but none of Beardslee's family was present.
Up to 300 opponents of the death penalty staged a demonstration outside the prison.
Beardslee's attorneys had argued he was duped by accomplices and was suffering from mental illness aggravated by brain injuries when he shot Stacey Benjamin, 19, and choked and slashed the throat of Patty Geddling, 23, in California in 1981.
The air force veteran, who was out on parole at the time for a 1969 murder of a young woman in Missouri, confessed to both killings and was sentenced to death in 1984.
"The state and federal courts have affirmed his conviction and death sentence, and nothing in his petition or the record of his case convinces me that he did not understand the gravity of his actions or that these heinous murders were wrong," Schwarzenegger said in a statement on Tuesday.
Beardslee's attorneys had asked the governor to commute his sentence to life in prison without parole.
In a five-page response, Schwarzenegger detailed the brutality of Beardslee's three killings, and rejected the argument that the killer was mentally impaired.
"We are not dealing here with a man who is so generally affected by his impairment that he cannot tell the difference between right and wrong"
Arnold Schwarzenegger, California governor
"We are not dealing here with a man who is so generally affected by his impairment that he cannot tell the difference between right and wrong," he said.
Also on Tuesday, the US Supreme Court rejected Beardslee's request for a stay of execution, turning down his appeal without any comment or recorded dissent.
Beardslee was the 11th inmate executed since California restored the death penalty in 1978. He was one of 640 people on California's death row, the largest in the nation. Texas is second with 455.