The 56-year-old, who has held the role since 2001, was confirmed in his position for the next three years after securing every single vote of the members with only one abstention - his own.
He was joined on the board by Dr Jens Buchta, who replaces Peter Lange, and Ulrich Kollmann.
Speaking to the members inside the Emscher-Lippe-Halle, Tonnies looked back on a successful season, in which the team finished third in the Bundesliga and qualified for the Champions League next term.
"It was a strenuous and, to begin with, turbulent season," he said on his club's website. "And we ended it with great success."
Looking forward to next season, Tonnies wants Schalke to set an example both on and off the field.
"Schalke has got to stand up and there has got to be a rethink in the minds of those who have not yet understood - fire is dangerous," he said, referring to the ongoing problem of pyrotechnics in German football.
"It has got to be possible for parents to send their children to the ground without having to worry.
"Otherwise, there is nothing that worries me about our club."