Western United have missed the opportunity to finish third in their maiden A-League campaign as second-placed Melbourne City picked up a deserved 3-1 victory in the final match of the regular season.

A second-half double from Jamie Maclaren and an early goal from Moudi Najjar proved enough for City to clinch the win at Netstrata Jubilee Stadium on Wednesday night.

Maclaren's strikes ensured the Socceroos striker would claim the A-League Golden Boot award with 22 goals, clear of Sydney FC's Adam Le Fondre (20) and Western United's Besart Berisha (19).

The result means Western United will tackle Brisbane Roar on Sunday, with Wellington Phoenix facing Perth Glory in the other elimination semi-final on Saturday.

Western United went into the contest as the A-League's form team with four wins from five matches since the competition's restart.

However, Western coach Mark Rudan chose to field a hugely inexperienced line-up after a heavy schedule with barely a regular in the starting side and star personnel such as Alessandro Diamanti and Berisha both on the bench.

Melbourne City lined up with youngsters Connor Metcalfe, Najjar and Stefan Colakovski in place of Florin Berenguer, Lachie Wales and the suspended Craig Noone.

Western's youngsters made a poor start, turning over possession and allowing Najjar to fire home from inside the penalty area on 12 minutes for his maiden A-League goal.

City dominated for lengthy periods although Western goalkeeper Filip Kurto was stretched only on a few occasions, notably to keep out a Nathanial Atkinson strike.

Acting Western captain Aaron Calver produced one of the more unlikely clearances, somehow heading over his own crossbar despite lying on the ground, with Maclaren set for a tap-in.

City turned up the heat after the break although their second goal came in somewhat fortuitous circumstances.

Tomislav Uskok was deemed guilty of handball after a Harrison Delbridge header struck him at point-blank range, allowing Maclaren to thump home from the penalty spot.

Diamanti and Berisha entered the fray soon after and Western finally started to enjoy some strong moments in attack.

Berisha needed just five minutes to pull a goal back with his own penalty after he was fouled in the penalty area.

It briefly threatened to be the second match in succession that City have given up a 2-0 lead to draw 2-2.

But Maclaren sealed the contest with a tap-in after Wales provided a perfect low cross with four minutes remaining.

The result means Western United missed the opportunity for a clean sweep of wins over the other teams in the top six.