Khelaifi, a Qatari with close ties to the Gulf state's royal family, is under investigation for allegedly bribing disgraced former Fifa secretary general Jerome Valcke in exchange for World Cup media rights.
Khelaifi and his legal team arrived at the Swiss attorney general's headquarters in the capital Bern at about 9.30am, avoiding the main entrance and two dozen reporters gathered outside.
He emerged nearly eight hours later to proclaim his innocence.
"I have nothing to hide," the 43-year-old told reporters.
"I asked to come to Switzerland to explain myself. I am at the disposal of the attorney general if he wants to see me again...
"I came relaxed and I am leaving relaxed."
Khelaifi and Valcke, Sepp Blatter's former right-hand man, have been under investigation since March.
Swiss prosecutors allege that they engaged in corruption, bribery, criminal mismanagement and forgery of a document in connection with the awarding of broadcast rights for the 2026 and 2030 World Cups.
The attorney general's office (OAG) went public with the case on October 12th, announcing that authorities in France, Greece, Italy and Spain had cooperated with the probe, including by raiding properties.
Swiss prosecution spokesman Andre Marty said there was "huge complexity in the case" with "masses of information" to be sorted.
Following the day long interrogation, prosecutors have no immediate plans to question Khelaifi again but further interrogation remained possible, Marty explained.
"Mr. Al-Khelaifi was cooperative. He was answering to the questions," Marty said. "It's always nice to avoid a situation of total confrontation.
"Now it's up to the attorney general of Switzerland to see if his behaviour violated the law."
Once the probe is complete, the OAG must decide whether to drop the case or take it to court, a process than can take multiple years.
The OAG also confirmed that Fifa lawyers were present at the hearing, as the integrity of contracts agreed by Valcke on behalf of world football's governing body is a central question in the case.
The beIN Media group, which is headquartered in Doha, has insisted that its World Cup rights deals were "advantageous for Fifa", rejecting any suggestion that it got favourable treatment.
The contract covers broadcasting rights for the MENA (Middle East, North Africa) region for the tournaments.
The Qatar broadcaster's offices in Paris have been raided at the request of Swiss authorities.
A raid was also carried out at a luxury Sardinian villa that, it is alleged, was put at the disposal of Valcke, who is serving a ten-year ban from all football-related activity over separate ethics violations.
The villa, set in lush grounds on the Mediterranean island and which has an estimated value of seven million euros ($8.3 million), is owned by an international real estate agency.
Valcke, a 53-year-old French national, has told the French sports newspaper L'Equipe that he "received nothing from Nasser".
An increasingly prominent figure in sports and media, Khelaifi oversaw PSG's 222 million-euro ($264 million) world record signing of Brazilian superstar Neymar in August.
PSG, who were bought by Qatar Sports Investments in 2011, are not implicated in the Swiss investigation.
The corruption accusations are the latest to rock world football which is still reeling from the events of 2015, when Fifa officials were arrested en masse at the governing body's annual conference.
They are also the latest allegations to target Qatar.
The Gulf state has found itself routinely accused of corruption since controversially winning the right to host the 2022 World Cup, charges it has always denied.