The chosen successor of retiring FIA president Max Mosley, Todt was seen by many as the continuity candidate. He gets a four-year term.
Before the vote, Todt said his team would look for consensus not confrontation.
"We want to further develop F1 so that it benefits all those involved, from teams to fans," he said.
"As the regulator of a hugely competitive and technically complex sport we will also establish an independent disciplinary panel to investigate breaches of the rules and to recommend the most appropriate response."
His plan includes commissioners for the various sports governed by the FIA, including F1.
He defeated former world rally champion Ari Vatanen, who campaigned on bring change and openness to the governing body.
The FIA general assembly has 221 delegates from sporting clubs in 132 countries. Todt won convincingly, 135-49, apparently recovering nicely from a perceived sag in support near the end of the campaign. Twelve voters abstained.
The campaign itself was marred by allegations of favouritism, intimidation and vote-buying.
FOTA chairman Luca di Montezemolo congratulated Todt on his victory in the FIA presidential election, saying he expects the incoming president to bring a climate open to dialogue and constructive collaboration with the teams and FOTA.
"Formula One is about to embark on a new phase," he said.
"All the stakeholders must work together with an eye to the future, to increase the credibility and interest generated by this sport, tackling the technical and environmental challenges that await it, while keeping unchanged, those characteristics that have made it one of the most popular disciplines on the world stage."
Vatanen expressed his doubts the new president would bring major change to the governing body.
"Let's hope I'm wrong," he said." He has got to renew it and if he doesn't get rid of the ancient guard and all the people who worked with Mosley, he won't succeed."
To complicate matters, Mosley stays on the scene in the FIA senate, and many feel he might still be able to exert influence on the organisation from that seat.