Magnussen was handed a 10-second time penalty for hitting RB rival Yuki Tsunoda during the restart of the race following the first safety car period.
As they exited Turn 6, Magnussen appeared to suffer a snap of oversteer and hit the right rear tyre of Tsunoda's car, sending the Japanese driver into a spin.
The damage caused to Tsunoda's car forced him to retire from the race straight away while Magnussen managed to keep going.
The Dane was found "predominantly to blame" for the accident by the stewards, who hit him with a 10-second time penalty.
Komatsu believes the penalty was too harsh, as he reckons it was just a racing incident.
"I do not think that's justifiable. I think it's just a racing incident," the Japanese team boss said.
"He didn't run Tsunoda off the track. He dived inside of Turn 6, he hit the apex, Tsunoda was wide, he still left the room, Tsunoda came back progressively.
"He doesn't go off the track, so maybe the definition 'came back' might be wrong. But it's not like Kevin is wholly to blame. For me, minimum 50/50.
"If anything, I think more Tsunoda's [fault]. Honestly, he didn't turn into Tsunoda or anything. He's dived inside, hit the apex, had a snap, but [it] didn't change the car direction. He didn't then run Tsunoda off the track.
"He has still room left. So why is that a penalty?"
Komatsu said that while the penalty was not appealable, the team would demand an explanation from race direction as he did not agree with the decision.
Magnussen, who finished the race in 16th place after his penalty, felt there was nothing he could have done differently to avoid the incident.
"I don't know. It seemed to me like he was going very wide. And then he made it stick anyway. And I was kind of locked in my rotation. I couldn't really do anything more. But they deemed it was a penalty for me. So it is what it is.
He added: "I think it feels like I did what I could to. When we had contact there was the car width [on the outside].
"So I think we just misread each other a little bit, I guess. I need to review it. But to me, it might as well have been a racing incident."
