Vincent Aboubakar found the net with a glancing header with ten minutes remaining, but Werner restored Germany's two-goal lead, ensuring their first-place position in the group and becoming the first German to score two goals in a single Confederations Cup match with his close-range, accurate finish.
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.
It was only after Cameroon's players insisted he review the incident again that he realised his error, rescinded Siani's sending off and instead flashed the red card to the correct culprit Mabouka.
Russian Federation had taken the lead in the 25th minute with a low strike by Alexander Samedov, beating goalkeeper Guillermo Ochoa just inside the far post after Mexico had failed to clear a header and midfielder Aleksandr Erokhin missed the ball as he was trying to shoot.
Cameroon pulled one back through Aboubakar, with a goal that Ter Stegen will not want to see again.
Any thoughts of a comeback from the 10 men, though, were quashed when Werner lashed home his second as Germany's young side went on to seal a comfortable win.
Two Dublin firms at centre of Di Maria, Ronaldo & Mourinho tax controversy
Ronaldo is accused of using a business structure created in 2010 to allegedly hide his image rights income between 2011 and 2014. And Salgado, speaking to reporters in Guatemala, echoed those sentiments and said: " Real Madrid do not want Cristiano to leave".
"I have asked Federation Internationale de Football Association to leave the system at the four stadiums and FC Krasnodar has asked for it as well", Mutko told reporters in Kazan ahead of Russia's final Confederations Cup group stage match against Mexico.
James Troisi steered Australia ahead after 42 minutes in Moscow, but Chile replied through half-time substitute Rodriguez on 67 minutes to progress as Group B runners-up behind Germany.
Cameroon goalkeeper Fabrice Ondoa prevented Germany from extending its lead by blocking Kimmich's shot from a tight angle.
The blunder by Ter Stegen for Cameroon's goal should concern Loew. The South American side defeated Cameroon 2-0 in the first match day and tied 1-1 against Germany in its latest encounter.
"I'm very happy to be Chile's top-scorer now, our dream is to win this tournament and we feel we have a chance", said Sanchez, who refused to be drawn about his Arsenal future.
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