The Natick football team will not be penalized by the Massachusetts Interscholastic Athletic Association for using an unauthorized ball in Tuesday night’s Division 2A playoff game — a 38-33 win over Plymouth South at Braintree High.

Citing inclement weather conditions, the back judge granted Natick permission before the game to use a Wilson GST ball, a brand the majority of high school teams use during the regular season. The official was not aware that MIAA tournament rules require teams to use the Spalding J5V. During the game, each team supplies the ball for its own offense.

Plymouth South coach/athletic director Scott Fry and other athletic directors for each playoff-bound school, including Natick, were handed a J5V ball at a meeting at the MIAA office in Franklin on Monday. Each school was told the J5V was the only ball allowed in the playoffs, and Plymouth South used that ball the entire game on offense. Natick athletic director Tim Collins issued a statement Wednesday night that did little to explain why Natick used a ball it was told not to on Monday.

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With four minutes left in the fourth quarter, Fry was informed by one of his captains that Natick was using an unauthorized ball, prompting assistant coach Walter Fust to approach Paul Peters, the MIAA site director and a former AD at Natick.

Peters confirmed with game officials that Natick had been using the Wilson GST the entire game, and a 15-yard unsportsmanlike conduct penalty (illegal equipment) was assessed to the Redhawks.

After a Natick punt, Plymouth South drove the length of the field for a score, closing the deficit to 38-33. But Plymouth South failed to recover an onside kick and ultimately lost by that score.

On Wednesday, Richard Pearson, the MIAA associate executive director, told Plymouth South principal Patricia Fry (Scott Fry’s wife) that because Natick received permission prior to the game to use the ball, the game result will stand. In addition, the MIAA uses NCAA rules, and there is no appeal process for a situation such as this.

Natick (11-1) will play Beverly (12-0) in the Division 2A Super Bowl Saturday at Gillette Stadium.

“It’s kind of a cloud that’s hanging over us,” Scott Fry said. “It’s unfortunate, because it was a well-played game by both teams.”

After Plymouth South clinched its first MIAA tournament berth with a 13-12 win over Nauset Nov. 9, it ordered three Spalding J5V balls to use in practice.

“I’ve known this rule as a football coach for years,” Fry said. “I had never been in the tournament and I knew the rule.”

According to Fry, the Wilson GST, which his team used the entire regular season, has texture and laces that make it easier to handle than the Spalding J5V in inclement weather.

Using the Wilson GST, Natick’s Troy Flutie completed 17 of 25 passes for 278 yards and four touchdowns.

After the game, Natick receiver Brian Dunlap told the Globe, “Troy did a great job throwing the ball, it was just like a regular day.”

Coach Mark Mortarelli added, “Troy was so accurate.”

Patricia Fry said, “It’s tough because we’re asked to follow all the same rules for a reason. This is something that shouldn’t have happened.”

Plymouth South, however, accepts the MIAA’s decision.

“This isn’t sour grapes,” Fry added. “It’s the MIAA’s decision, it’s out of our hands. We wish [Natick] well on Saturday.”

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Billerica announced that Peter Flynn was retiring as football coach after 23 years. Flynn went 150-96 with just four losing seasons and two Super Bowl titles.

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The appeal was emotional and sometimes confrontational, but the majority of the penalties imposed on Gardner last month by the MIAA Board of Directors was upheld Wednesday at the board’s monthly meeting in Franklin. The penalties center around former Gardner swimming coach Don Lemieux and violations of the MIAA’s bona fide team rule, which restricts students from missing a high school game or practice to participate in a non-school athletic event.

Gardner superintendent Carol Daring, principal Donna Pierce, and former interim athletic director Tim McCormick appeared before the board to appeal the Oct. 22 penalties. After a hearing, the only penalty the MIAA reversed was allowing Gardner to host a cooperative swim program this winter. The change allows swimmers from other schools to compete with Gardner but it does not affect Gardner students.

The penalties that remain in place include forfeiture of regular-season meets, forfeiture of the 2012 sectional title and trophy, and two years’ probation.

The board voted to allow softball teams to use metal cleats and toe plates in the spring.