The German 2014 World Cup winner married former Miss Turkey Amine Gulse in a ceremony at the luxurious Four Seasons hotel on the Bosphorus.
Ozil, who is third-generation Turkish-German, sparked controversy in his birth country in March when he announced Erdogan would be his legal witness.
The roles, reportedly required of one man and one woman for secular Turkish weddings, are often filled by people close to the couple.
German Chancellor Angela Merkel’s chief of staff, Helge Braun, said the selection “makes one sad,” the country’s Bild newspaper reported shortly after the announcement
Before entering politics, Erdogan was a semi-professional footballer, and he often poses with prominent players of Turkish descent.
Ozil and German teammate Ilkay Gündoğan were heavily criticized for posing with the President before the 2018 World Cup.
“I am German when we win, but I am an immigrant when we lose,” he said, lashing out in a letter posted online.
Erdogan, now in his fifth year in office, is a polarizing figure. Supporters say he has improved the Turkish economy and introduced political reform.
Critics accuse Erdogan of autocratic tendencies, corruption and extravagance. He has also been heavily criticized for failing to protect women’s and human rights, curbing freedom of speech and attempting to restrain Turkey’s secular identity.
Ozil’s management was not immediately available for comment on Erdogan’s attendance at his wedding.
Charity efforts mark wedding bliss
The newlyweds made sizable donations to the Turkish Red Cross, partly in an effort to feed thousands of Syrian refugees living along the Turkish-Syrian border.
Ozil also went online to encourage fans to match his donations to BigShoe, a charity that funds emergency operations for children in need.
“As a professional footballer I am in a fortunate and privileged position,” he wrote on Twitter. “However, I invite everyone who is willing and able to help to support a very special project close to both of our hearts.”
“Amine and I will bear the expenses for surgeries of 1000 children in need.”