Swinney said Tuesday that there was defensive pass interference on Clemson receiver Artavis Scott, who made contact with Alabama cornerback Marlon Humphrey and created some traffic that another Alabama defensive back got caught in on Hunter Renfrow's 2-yard TD catch with a second left Monday night.
Clemson beat Alabama 35-31 in the College Football Playoff National Championship presented by AT&T to win its first national title since 1981.
"Yes, it's a rub play, it's a pick play," Swinney said Tuesday. "Artavis was actually trying to go pick the guy, but he couldn't get there because he got tackled. I mean, literally, the guy tackles him."
Alabama players and fans did not quite see it that way, and thought Clemson should have been flagged.
"Usually, on a pick route, you're not supposed to chop somebody," Alabama linebacker Tim Williams said.
"They were getting a lot of calls," Crimson Tide defensive back Hootie Jones said. "We felt like the refs were just against us. I'm not saying we got out of poise on our own. We felt like it was starting to be taken from us."
NCAA coordinator of football officials Rogers Redding, who was in the television booth for the game, said he has not studied the play but after watching it several times he called it a "sensible no-call."
"What the officials are looking for is who initiates the contact," Redding said. "If the receiver comes out and clearly blocks on the defender and the other receiver cuts off that block, then it's offensive pass interference.
"What we saw was the contact was either initiated by the defense or mutually initiated. It wasn't a play where the offensive player clearly came out and blocked on them."
Scott never made contact with Tony Brown, the defender who was guarding Renfrow. Brown had to go around Scott and Humphrey, like a basketball player going over a screen, and who could not get there in time. Renfrow was wide open.
The official rule is this: Offensive pass interference by a Team A player beyond the neutral zone during a legal forward pass play in which a forward pass crosses the neutral zone is contact that interferes with a Team B eligible player. It is the responsibility of the offensive player to avoid the opponents.
"I mean, if you really watch the play, we never even got a chance to really rub the guy (Brown)," Swinney said. "But he had to play over the top. That's the way the play is designed."
Said Humphrey: "They were somewhat legal, but I mean, I'm not a ref. They have a little better view than I have. So ... they did a pretty good job on that."
The Associated Press contributed to this report.