A $3.5 million pedestrian underpass at the Marion Railway Station will be built, despite widespread opposition from residents, local schools and Marion Council.
The State Government said plans for an underpass were approved by Transport Minister Tom Koutsantonis and the Development Assessment Commission last week.
Work is expected to begin on the 4m wide by 30m long underpass later this month.
The underpass will replace an existing overpass, which will be removed because of work associated with the electrification of the Seaford line.
Marion resident Samantha Kerr said she was "angry and disappointed" at the decision as it went against the wishes of the community.
"We were expecting a different result, especially as so many people came together to show their opposition to the underpass," Ms Kerr said.
She said the community was united in its opposition to the underpass, over safety concerns and fears it would attract vandalism and criminal behaviour.
"We were told the underpass would be put on hold pending a review but it is difficult to see that what we've said has been listened to or taken into consideration,'' she said.
"We are not just a couple of residents, it was hundreds of residents, the head of Westminster School, the local member Pat Conlon and Marion Council."
Mr Koutsantonis said safety of commuters was behind the final decision.
"In choosing the design approved by the Development Assessment Commission, we have at
all times stressed that the highest priority is the safety of rail customers, staff and the public," Mr Koutsantonis said.
"I am confident the approved design is the best and safest solution for this location.
"Grade separation removes the possibility of pedestrians and trains being at the same time
and space where a collision is physically possible."
The government was forced to put its underpass plan on hold in June after a groundswell of opposition from nearby residents who wanted electronic gates, similar to those at the Oaklands Railway Station.
Westminster School argued for a replacement of the overpass, and Marion Council's preferred option was electronic gates and an underpass.