Local media Geo TV reported that the trial court in Islamabad cancelled the warrants for his arrest as a result of his presence on Saturday.
Khan, in office from 2018 to 2022, is facing a spate of legal challenges, including one that prompted a failed attempt to arrest him on Tuesday, sparking clashes between supporters and police, which also took place on Saturday.
Khan's aide Fawad Chaudhry told Reuters the former premier's presence had been recorded officially by the court and he had left to return to his home in the city of Lahore.
According to local media, Khan's vehicle reached the judicial complex in Islamabad amidst clashes between police and his supporters. They reported that, given the chaos around the complex, he was unable to physically enter the courtroom, and was ultimately allowed by the judge to sign his presence from his vehicle.
He was ordered to address charges in court on Saturday of unlawfully selling state gifts given to him by foreign dignitaries while in office.
Khan says he followed legal procedures in acquiring the gifts.
Earlier in the day, police had entered Khan's home in Lahore after he left for his court appearance in Islamabad and arrested several of his supporters over allegations of attacks against officers during clashes earlier in the week.
Prime Minister Shehbaz Sharif took to Twitter to criticise Khan, saying he was using people as human shields and was attempting to intimidate the judiciary.
Khan has led nationwide protests since his ouster from power last year and has had a spate of cases registered against him.
Earlier this week, police and Khan's supporters clashed outside his home during the arrest attempt.
Hours before leaving his home, the former cricket star told Reuters he has formed a committee to lead his party, the Pakistan Tehreek-e-Insaf (PTI), if he is arrested.
Khan, who was shot and wounded while campaigning in November, said in the interview the threat to his life is greater than before and asserted - without providing evidence - that his political opponents and the military want to block him from standing in elections later this year.
The military and government did not immediately respond to requests for comment.
On his assurance that he would appear on Saturday, the court granted Khan protection against arrest, but he said he feared the police and government planned to take him into custody.
"It is now clear that, despite my having gotten bail in all my cases, the (Pakistan Democratic Movement coalition) govt intends to arrest me. Despite knowing their malafide intentions, I am proceeding to Islamabad & the court bec(ause) I believe in rule of law," Khan said on Twitter.
"It is also obvious now that the entire siege of Lahore was not about ensuring I appear before the court in a case but was intended to take me away to prison so that I am unable to lead our election campaign."
