The 2014 Super League champions signed the 28-year-old Australian on a two-and-a-half-year contract just over a month ago after taking advantage of the amended marquee player rule introduced by clubs earlier in the year.
However, the Darwin-born Barba, a Grand Final winner with Cronulla last September, arrived via French rugby union club Toulon with a hefty suspension hanging over him following his use of cocaine.
The Rugby Football League decided to honour that ban imposed by the NRL and an independent operational rules tribunal, sitting in Leeds on Tuesday evening, dismissed Saints' appeal.
A statement from the RFL said: "The independent panel, led by His Honour Judge Peter Charlesworth, confirmed the suspension originally set by the NRL and subsequently recognised by the Rugby Football League, should remain."
Barba has already sat out five games and will now be available for round four of the Super 8s in the week beginning Monday, August 28.
St Helens, who beat rivals Warrington to the prized signature of Barba, argued that, had the player been caught using cocaine in an out-of-competition test in England, he would have avoided a ban.
The RFL had to weigh that up against loyalty to their NRL counterparts, who could have been expected to receive their backing.
The governing body were loathe to be seen to be undermining the authority of the NRL, who insisted the player would still have to serve his 12-match ban if and when he returns to Australia if he was allowed to by-pass it in Super League.
Barba recorded a second strike under the NRL code's illicit drugs policy last November and was released by Cronulla after the Sharks' historic triumph over Melbourne, opting to take up a rich deal in the Top 14 competition to secure the financial future of his family, including four daughters.
Barba, who won the Dally M Medal award for best player of the year in 2012 while he was at the Canterbury Bulldogs and also played for Brisbane Broncos before joining Cronulla in 2015, made just four appearances for Toulon before being axed.
