Kumar, 56, also played a crucial role during weeks of demonstrations that led to the restoration of democracy after deposing Gyanendra in 2006.
The Maoists boycotted the vote after refusing to accept Kumar's candidacy.
Several Maoist politicians loyal to Nepal's Maoist Communist Party (UCPN-M) stormed out of parliament when the speaker declared that Kumar had been "elected unopposed".
Kumar's predecessor Pushpa Kamal Dahal, the leader of the UCPN-M, resigned on May 4 after the country's president stopped him from firing the army chief.
Though Dahal attempted to block parliamentary proceedings for Saturday's vote, he did put an end to protests several days ago that made Kumar's election possible.
Both Dahal's and Kumar's parties are communist but differ in policies and beliefs.
The Maoists ended their decade-long armed struggle three years ago and entered a peace process.
They won general elections in 2008 but were not able to obtain a majority in parliament.