Chile, who face European champions Portugal in the last four on Wednesday in Kazan, came second in the group with five points, two behind Germany and three ahead of Australia in third.
The result means Low's men progress as Group B winners and return to Sochi's Fisht Stadium on Thursday to face Mexico in the semi-finals.
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Germany took the lead in the 48th minute through Kerem Demirbay.
After a VAR review saw Ernest Mabouka eventually sent off for a high tackle on Emre Can after Sebastien Siani was initially mistakenly dismissed, Germany quickly extended their lead through Werner's first global goal.
Cameroon were gifted a way back into the match when Marc-Andre ter Stegen let Aboubakar's header burst through his gloves in what was a poor goal to concede for the Barcelona keeper.
Werner then gave Germany a two-goal cushion with a diving header, his first goal at senior global level, from Joshua Kimmich's cross on the right wing.
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Ter Stegen prevented Cameroon going in front, with the goalkeeper's one-handed save blocking Andre-Frank Zambo Anguissa's hooked shot across goal at the end of a nervy first-half for the Germans. Julian Draxler fed Demirbay with a back-heel through Siani's legs and the midfielder marked his first global start by slicing a shot into the top corner with his weaker right foot.
Follow the Football match between Germany and Cameroon live with Eurosport.
Troisi's 42nd-minute goal put the pressure on Chile, which responded well and would have equalized through Vidal just before the break, but for Dylan McGowan's last-ditch block. The striker whose goals propelled Leipzig to a surprise second-place finish in the Bundesliga turned a cutback from Benjamin Henrichs into the net.
"I have to say I am very proud and full of praise for the team for reaching the semi-finals", said Loew. "They're under pressure. You've seen that we caused them some real problems, that we matched a world-class team".
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