Samoa scored four tries to Tonga's three but missed three of four conversions in their 20-18 World Cup quarter-final defeat.
Chanel Harris-Tavita left the field clutching his hamstring, and Ronald Volkman missed a conversion after Hamiso Tabuai-Fidow's try.
Volkman later scored and converted to put Samoa ahead with less than 12 minutes remaining.
Tonga prop Addin Fonua-Blake settled the contest with a try in the 72nd minute at CommBank Stadium, watched by 29,411 spectators.
Kristian Woolf's team maintained its unbeaten group-stage record and will meet New Zealand in Newcastle on Saturday.
The semi-final will be the nations' first World Cup meeting since 2017, when Jason Taumalolo-led defections to Pacific teams shaped the tournament.
Taumalolo impressed for Tonga, while Harris-Tavita now appears unlikely to face Australia in Samoa's semi-final.