Warnig's promotion marks only the latest step up the ladder of major Russian business for the former Dresdner Bank Group member.
The 57-year-old already serves as managing director of the Nord Stream AG's operator of Russia's new Baltic Sea natural gas pipeline to Germany that was unveiled last year.
He is also the chairman of the Transneft state oil pipeline monopoly and board member of the Rosneft energy giant as well as two major banks and smaller companies.
Warnig replaces interim chief Barry Chung at the seat of power of tycoon Oleg Deripaska's major holding – a company in crisis because of raging disputes over how to handle more than $10 billion of debt incurred in the 2008-2009 financial crisis.
"Mr Warnig has significant public company experience having served on the board of several leading international companies," Rusal said in a statement.
"He has an excellent knowledge of Russian and international business and an in-depth understanding of the financial, energy and commodity industries."
Deripaska's En+ Group through which he controls Rusal pointed to the unanimous boardroom vote as "an example of constructive cooperation" that follows the resignation of former powerful board chair Viktor Vekselberg.
It was Vekselberg's shock decision to step down in March that originally exposed the extent to which Russia's richest men disagreed over ways to manage production of nine percent of a metal that goes into everything from autos to planes.
Vekselberg at the time said Rusal was in "deep crisis." Deripaska then went on to sell top oversees production units as a cost-cutting measure that sparked even more displeasure from minority shareholders.
The appointment should now make it easier for Rusal to maintain close terms with the Kremlin at a point when it is trying to stave off disintegration.
Warnig has long been reputed to have special personal ties to Putin despite his refusal to go into the subject in any great detail.
The strongman leader has seen several of his old school friends and acquaintances claim top posts in business and government since first rising to power in 1999.
Critics condemn this as cronyism but Putin himself – viewed as the ultimate arbiter in Russian business disputes – has dismissed all charges.
Warnig has been linked to Putin repeatedly by both Russian and Western media over the years.
One former Dresdner Bank executive told The Wall Street Journal in 2005 that Warnig had alluded to his Stasi connections but that German investigators eventually dropped the case.
The Wall Street Journal said at the time that Warnig and Putin, a former Soviet intelligence agent who was based in Dresden, jointly recruited East Germans to work for the KGB.
Moscow's Kommersant business daily reported that Warnig became a Stasi major before retiring in 1989 in the months preceding the fall of the Berlin Wall and before switching his focus on Russian business.
The official biography released by Rusal featured a gap in Warnig's career between his university graduation in 1981 and 1993.
The Wall Street Journal said he opened the first Dresdner Bank in Putin's native city of Saint Petersburg in 1991 and in 2008 was appointed to the board of Bank Rossiya – a lender founded by Putin's friends.