Lance Corporal Daniel Smith, 21, was also ordered to pay $2,000 to the defendant for raping her while she was drunk.
Three other marines who were accused of doing nothing to help the woman, were acquitted.
Smith was accused by the 23 year-old Filipina of sexually assaulting her on November 1 last year while she was intoxicated.
Smith said the sex was consensual. Staff Sergeant Chan Carpentier, Lance Corporal Keith Silkwood and Lance Corporal Dominic Duplantis backed up his testimony.
The lengthy judgment, read out by a court employee, was televised live nationwide.
Güncelleme Tarihi: 20 Eylül 2018, 18:16
"He was the one who was on top of the complainant, who resisted his kisses, pushed him and fought him back until she lost consciousness because of alcoholic drinks she had taken," it read.
It also said that "Nicole", known by her pseudonym in the case, was so intoxicated that she could not have consented to sex, pointing to a testimony that Smith had carried her to a van where the incident occurred.
It was unclear whether Smith would serve the sentence in the Philippines or elsewhere.
The case had strained ties between the Philippines and the US.
About 100 protesters outside the courthouse chanted slogans that read "Justice for Nicole, justice for our nation. Scrap VFA", referring to the 1998 Visiting Forces Agreement for joint military exercises with foreign troops.
Critics say the VFA favours the US and grants its troops unfair protection against prosecution.
Smith is first American soldier to be convicted of wrongdoing in the Philippines since Manila closed down US bases in the early 1990s.