Images from the Friends Arena in the Swedish capital showed cops using batons on fans in the away section, while around eight flares were also lit in the away section of the stadium ahead of kick-off.
Three people are understood to have been arrested as a result of the skirmish, and the Hoops could face punishment from UEFA over the use of pyrotechnics and the disorder.
However, the champions are adamant that fans of AIK's rival club Hammarby, who also play in green and white, were able to get tickets for the away end and were ultimately responsible for the mayhem.
In a statement to the Daily Record, a spokesperson for Celtic said: “The club intends to launch a full investigation into the events in Stockholm.
“But the initial reports and intelligence we have gathered suggests that local supporters from a rival club may have been responsible for the unfortunate disturbances we witnessed.
"If that is indeed the case then obviously Celtic will strongly defend the reputation of our own supporters.
“It was clear many Hammarby fans were in the Celtic sections and this was raised by Celtic officials before the match. We are concerned that AIK sold tickets to locals in that section.
“A lot of Swedish fans managed to infiltrate the away section which we believe was a major factor in the issues which arose. There was a lack of control at the access points to the Celtic section.
“We are aware that a number of Swedish supporters entered the area for visiting fans and we are currently investigating events.”
Asked about the incident following Celtic's 4-1 win, manager Neil Lennon told the BBC: "I don't know what the issue was.
"How could I see it? I'm on the touchline. Our fans are impeccable [at away games], so I hope no one was hurt."
Celtic's 4-1 win on the night and aggregate 6-1 victory saw them safely through to the draw for the group stages, where they will be joined by rivals Rangers, who knocked out Legia Warsaw with a last-gasp winner from striker Alfredo Morelos.
Former Hoops goalkeeper Artur Boruc was among the away fans at Ibrox.
The draw for the groups takes place at 12pm BST tomorrow.