James Meredith came closest to breaking the deadlock during a cagey 90 minutes, Mariners goalkeeper Mark Birighitti making a stunning save from his towering header, but the Macarthur defender would not complete the match.
Meredith clumsily pulled back Marco Urena with 15 minutes of regulation remaining and referee Shaun Evans's assertion that it amounted to a professional foul was upheld by the VAR (video assistant referee).
Macarthur managed to see things through until the whistle and then hit the front three minutes into the first additional period via an own goal.
Substitute Ivan Franjic fashioned a cross from the right when there appeared to be little on and Markel Susaeta swept a shot against the post. Former Central Coast forward Charles M'Mombwa reacted quickest and his header was diverted in via the crossbar as Stefan Nigro desperately attempted to clear.
Kye Rowles blazed over for the Mariners after a 119th-minute scramble in the penalty box, but Macarthur made sure of a showdown with premier Melbourne City when Jake Hollman released fellow replacement Michael Ruhs to coolly convert in stoppage-time.