The ad, created by TBWA\London, ran on websites for Yahoo and BT, and showed a character called Kovac holding a knife and then a gun.
The ad carried on-screen text, which read: "You on my side? Listen up I've killed for less the music plays Puccini in my head...Kovac Mercenary or Misunderstood?".
In national press ads also backing the PS3 launch, Kovac was described as an orphan from age seven, who joined the Croatian Army 10 years later, but later deserted the Army to become a freedom fighter.
The wider campaign, which also included TV spots and other press and online ads, attracted a total of 23 complaints.
Some members of the public complained the internet ad featuring Kovac condoned and glamorised violence and anti-social behaviour, particularly among young people.
Other internet ads for the PS3, featuring images of a naked woman astride a man, and a character called Cherry sitting on the toilet, also attracted complaints.
However, these ads were not banned by the Advertising Standards Authority, with the watchdog ruling the ad showing Cherry on the toilet as "light-hearted and humorous", but unlikely to cause serious offence.
However, complaints about the internet ad featuring Kovac, which was shown on websites targeted at those over 18 years of age, were upheld. The ASA said the ad contained an "underlying tone of violence".
Other complaints about two TV spots for the PlayStation 3 were not upheld on the grounds that they were "surreal" in their approach and were aired with a post 9pm scheduling restriction.