Gordon and Johnson were battling for second place on lap 241 when the former seemed to get very close to the rear bumper of his team-mate's car between Turns 3 and 4, Johnson getting loose and allowing Gordon to dive on the inside of him.
The reigning champion apparently was not happy with the move and appeared to retaliate by hitting Gordon's right-side with his left-front.
The contact could have been costly for Johnson as he had to pit for a new left front tyre ahead of schedule, although caution flags later in the race would go his way to allow him to get back in contention for victory.
Meanwhile his team-mate, who went on to take the lead again following their clash, was unable to finish the race after being involved in a multi-car crash only 17 laps from the chequered flag.
After his retirement from the race, Gordon said he was disappointed with Johnson's aggressiveness towards him, although he expects both to get over the incident soon.
"He ran in to the back of me for no reason," said Gordon. "Then later he got out ahead of me after a pitstop or on a restart. He was just too loose. He wasn't fast enough and my car was just so good I could just get right to his bumper and he got loose.
"I guess he thought I was being too aggressive. I don't know, he just drove into my door. It ended up costing him. When you have a race car like that, you don't have team-mates and friends out there and race hard. That is what Jimmie has had."
"I am disappointed," he added. "But, I'll get over it and so will he. We'll talk about it. We are good enough friends, good enough team-mates. It is more just the competitors in us coming out there and the aggressiveness of wanting to win. Not anything against one another."
For his part, Johnson said he was disappointed with Gordon, although he reckons it is not the first time such an issue has occurred between them. He also expects the issue to get dealt with soon.
"Yeah, I mean, it's going to happen in racing," said Johnson. "Doesn't matter if it's team-mates or not. There are just times where you're irritated by racing with other guys. You know, Jeff and I have been racing hard against each other for wins for a long time. We've had this issue in the past, so I really don't see it being a big deal.
"I guess he got out and said he was disappointed. So since I have my chance I can equally say I was pretty disappointed with him today. We'll sit down and get it talked out."
Gordon currently ranks fifth in the Sprint Cup standings, which continue to be led by Johnson ahead of next weekend's race at Talladega.
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