Ruggiero had been considered the favourite to take up the role, with the American having been serving as the Commission’s vice-chair, with the position also seeing her join the IOC Executive Board.
The 36-year-old, who won gold at the Nagano 1998 Winter Olympics, was elected following a vote by the members of the Commission.
She was appointed as the chief strategy officer of the Los Angeles 2024 Olympic bid in May, with her role claimed to be centred around addressing "the needs of the Olympic Movement in the post-Olympic Agenda 2020 landscape."
Paris 2024 co-chairman Tony Estanguet, a three-time Olympic canoeing gold medallist, has been elected as vice-chair, raising questions over two bid rivals working together.
But Ruggiero laughed off any questions about this, telling insidethegames that it will be the "Olympic spirit of friendly competition in action".
"I think, immediately, doping is our biggest priority," she added.
"We want to have an integral part of the discussions as we go forward, because this is the most important issue for athletes today."
Ruggiero has been a member of the IOC since 2010, when she was elected to the body's Athletes’ Commission, with the American chairing the Coordination Commission for the Lillehammer Youth Winter Olympics, which took place in February.
She will become the second American women on the IOC Executive Board along with Anita DeFrantz.
This comes as the role of the Athletes' Commission becomes increasingly important following the Russian doping allegations which are threatening to rip apart the Olympic Movement.
Bokel, who led the Commission for four-years, will step down from the post and the Executive Board after her term officially draws to a close at the end of the Rio 2016 Olympic Games.
She abstained from the recent IOC decision not to hand Russia a blanket ban from Rio 2016, but has received criticism from some quarters for her lack of vocal responses in comparison with World Anti-Doping Agency Athletes Committee counterpart, Beckie Scott.
But she is now on a three-person IOC panel making final decisions on Russian eligibility at Rio 2016.
Ruggiero also suggested that they will continue to combine ttaking a strong anti-doping line, with playing the political game, suggesting she will take a similarly non-controversial stance in public as that displayed by Bokel.
"It is behind the scenes you get things done in this world," she said.
Better organising the Commission's role in the sports world is another aim, as well as improving athlete representation in other bodies, such as International Federations and National Olympic Committees.
Elections will be held for new IOC Athletes' Commission positions during Rio 2016.