Faruk Koca has resigned as president of Ankaragucu after punching a referee at the end of a Super Lig match on Monday night.
Matches in all Turkish football leagues were suspended indefinitely by the country's football association after Koca ran onto the pitch and struck official Halil Umut Meler following their top-flight game against Rizespor.
On Tuesday, a Turkish court ordered the arrest of Koca and also remanded in custody two other suspects over the violence, the justice minister Yilmaz Tunc revealed.
Tunc said Koca and two others were formally arrested for "injuring a public official" after prosecutors took statements from them.
In a letter confirming his resignation, Koca wrote: "After the match we played against Çaykur Rizespor last night, due to my attitude towards the referee Halil Umut Meler, who managed the match, Mr. Meler and his family, in particular; I apologise to the Turkish referee community, sports public and our nation.
"How and why the subject came to this point is independent of the event. No matter how great injustice or wrong it is, nothing can legitimise or explain the violence that I committed, which I definitely did not desire.
"Sports fields should be the venue for gentlemanly competition. Any attitude that casts a shadow on fairplay, including my own, should not be present in stadiums or halls.
"As someone who has always taken constructive initiatives in this direction since the day I became the MKE Ankaragücü Presidency, I feel great embarrassment for having caused the creation of an exactly opposite environment.
"I would like to announce to the public that I have resigned from the MKE Ankaragücü Presidency in order to prevent any further harm to the Ankaragücü club, Ankaragücü fans, the community I am in and my family.
"I hope that this incident, which I, more than anyone else, cannot accept, will be a reason for our sports life, especially our football community, to be purified from mistakes, shortcomings and the culture of violence.
"At the same time, I hope that the structural problems of Turkish football will be discussed more realistically due to this grave incident that I caused.
"I would like to take this opportunity to apologise again to everyone I have upset, especially Ankaragücü fans.
"I would like it to be known that I am deeply saddened that both the club I manage, the football community, and our country are remembered with such an event and image."
Koca's side had conceded a 97th-minute equaliser, ensuring Rizespor would stay four points clear of their hosts after the 1-1 draw.
Ankaragucu fans invaded the pitch after the game and Meler was also kicked when he fell, though it was unclear who his assailants were. Meler eventually made it to the dressing room with the help of the police.
In a statement released several hours after full-time, the Turkish Football Federation said it condemned the "inhumane and despicable" attack on the official.
"We are following Halil Umut Meler's health condition closely and wish a speedy recovery to our valuable referee.
"This inhumane and despicable attack was made against all stakeholders of Turkish Football. Everyone who has targeted referees and encouraged crimes against referees is complicit in this despicable crime.
"The irresponsible statements of club presidents, managers, coaches and TV commentators targeting referees have paved the way for this vile attack today.
"In coordination with our state, all criminal proceedings deserved have been initiated against those responsible and instigators of this inhumane attack.
"The responsible club, the club president, its managers and all the criminals who attacked Halil Umut Meler will be punished in the most severe way.
"By the decision of the Turkish Football Federation Board of Directors, matches in all leagues have been postponed indefinitely."
FIFA president Gianni Infantino also condemned the attacks, saying: "There is absolutely no place for violence in football, on or off the field. Events following the Turkish Super Lig match between MKE Ankaragucu and Çaykur Rizespor are totally unacceptable and have no place in our sport or society.
"Without match officials, there is no football. Referees, players, fans and staff have to be safe and secure to enjoy the game, and I call on the relevant authorities to ensure that this is strictly implemented and respected at all levels."
Howard Webb, chief refereeing officer of PGMOL, said: "PGMOL stand in solidarity with our refereeing colleagues in Turkey and in particular Halil Umut Meler, who was the subject of a shameful attack following a Turkish Super Lig game last night. We wish Halil a full and speedy recovery.
"There is no game without match officials. Like all participants, they need to be valued and respected for the good of the game."
Turkey's football federation (TFF) has decided to hold an extraordinary meeting following the trouble, the country's public broadcaster TRT said.
The incident quickly reached as far as Turkey's president, Recep Erdogan, who was quoted in Turkish media condemning the attack.
"I condemn the attack on referee Halil Umut Meler after the MKE Ankaragucu-Çaykur Rizespor match played this evening, and I wish him a speedy recovery," said Erdogan.
"Sports means peace and brotherhood. Sports are incompatible with violence. We will never allow violence to take place in Turkish sports."
A detention order has been issued for Koca, Interior Minister Ali Yerlikaya said in a post on X, adding that two people have already been detained as part of a judicial investigation into the incident.
Two hours after the match finished, Ankaragucu's official account on X, formerly known as Twitter, issued an apology to the country's footballing community for the incident.
Originally written in Turkish, the statement read: "As MKE Ankaragücü Sports Club, we are saddened by the incident that took place this evening.
"We apologise to the Turkish football public and the entire sports community for the sad incident that occurred after the Caykur Rizespor match at Eryaman Stadium."
A FIFA referee since 2017, 37-year-old Meler took charge of Lazio's Champions League group game with Celtic on November 28.
Referees in Turkey are often criticised by club managers and presidents for their decisions but are rarely the target of violent attacks.
Ankaragucu are 11th in the Super Lig on 18 points, three places below Rizespor who have 22 points from 15 matches.