The Turkish soccer federation released a statement confirming Ozdilek's resignation but gave no other information.
FIFA is investigating the brawl between players and officials in Istanbul. FIFA's president Sepp Blatter has said Turkey may be banned from the 2010 World Cup as punishment.
Turkish newspaper reports said the brawl started after Ozdilek tried to trip a Swiss player running off the field.
Television footage showed Switzerland midfielder Benjamin Huggel kicking Ozdilek with Turkey's Alpay Ozlan trying to kick Huggel in retaliation and other players getting involved.
Switzerland qualified for next year's World Cup on away goals despite losing the match 4-2.