Magincalda, who was to be freed on Friday, was acquitted of murder but also found guilty of larceny and housebreaking, and cleared of making a false official statement.
The Iraqi civilian was pulled from his home in April 2006 and shot in a hole, with an AK-47 and shovel placed nearby to make him look like an anti-government fighter planting a bomb, according to the prosecution.
Prosecutors initially identified the victim as Hashim Ibrahim Awad, 52.
The name, however, was dropped from charge sheets.
In another Camp Pendleton courtroom, a jury continued deliberating on Friday over the sentencing of Sergeant Lawrence G Hutchins III.
The previous day, Hutchins became the first and only member of the squad to be convicted of murder in the killing.
He had been charged with premeditated murder but the jury struck the premeditation element, meaning Hutchins no longer faces a mandatory life sentence.
Testimony from several of his comrades pointed to him as being the mastermind of the plot to kidnap and kill the suspected anti-government fighter.
Hutchins was also convicted of conspiracy to commit murder, making a false official statement and larceny.
He was acquitted of kidnapping, assault and housebreaking.
Four lower-ranking marines and a navy corpsman cut deals with prosecutors in exchange for their testimony and received sentences ranging from one to eight years in prison.
A jury last month acquitted another corporal of murder but convicted him of conspiracy to commit murder and kidnapping.
According to testimony, Corporal Trent Thomas of Madison, Illinois, had greater involvement in the killing than Magincalda, of Manteca.
Thomas was sentenced to a reduction in rank and a bad-conduct discharge but no prison time.