Red Sox manager John Farrell stood firm in his stance that the New York Yankees’ Matt Holliday interfered with Sox first baseman Mitch Moreland during a strange play in the Sox’s 16-inning loss to the Yankees on Saturday.

The team took up their issue with the league office, protesting the game.

But after filing paperwork for the protest on Sunday, the Sox learned Monday that their petition was denied.

The bizarre play occurred in the 11th inning with Holliday sitting on first base. Jacoby Ellsbury sent a chopper down the first-base line, Moreland snagged it and fired to first to start a double play. Even though Holliday was already out, he retreated to first base, instead of removing himself from the play, sliding feet-first into the bag. In the process, he kept Moreland from receiving the throw from second and completing the double play.

It took nearly five minutes for the officiating crew to sort through a confusing situation and review the play. Ultimately, Ellsbury was ruled safe at first. The Sox played the rest of the game under protest of rule 6.01 (a), which outlines batter and runner interference.

Despite lengthy conversation between Red Sox president of baseball operations Dave Dombrowski and Major League Baseball’s chief baseball officer Joe Torre, the sides couldn’t come to an agreement on the interpretation of the rule.

“The ground that we took obviously wasn’t agreed upon,’’ Farrell said before the Red Sox’ 4-3 loss to the Blue Jays on Monday night at Fenway Park. “But there’s probably three or four different components in it. One is the actual interpretation. Two, is there a direct impact on the outcome of the game, and the other, I think, prominent words in the rule is that when there’s a runner that is advancing. In this case, there was a runner that was retreating. But that was oil and water in terms of the two sides.’’

Not long after the Sox decided to protest, the Milwaukee Brewers reached out to make them aware of a similar play involving Holliday from the 2015 season. Farrell said part of contesting the play was making sure it was on the league’s radar so it could be addressed going forward.

“I think any time you run into a situation where there’s a potential of [instructing] your runners to do a certain thing — in other words, instruct them to carry out this play — that’s where I think a lot of the debate or further conversation will come in,’’ he said. “So if there’s further rule clarity or terminology or verbiage, we’ll see where that goes.’’

Between a heated series with the Baltimore Orioles that prompted commissioner Rob Manfred to intervene in an argument between Farrell and umpire Bill Miller last month over a balk call to this most recent disagreement over the weekend, Farrell’s been on the phone with the league office more than usual this season.

He joked coyly, “I don’t know why.’’ Then he said, “There’ve been a couple things to come up. So every year’s going to have its different events whether it’s calls on the field to competitive environments you’re involved in, there’s been a little more frequency to it.’’

Rotation shift

A taxing 16-inning loss on Saturday followed by a doubleheader on Sunday forced the Sox to shuffle their rotation going forward. Brian Johnson will make a spot start Tuesday, taking the place of Doug Fister, who was scheduled to make his fourth start of the season before throwing 2⅔ innings on Saturday.

Fister will be pushed back to Thursday. The move will give an extra day’s rest to Chris Sale, who will pitch Friday against the Angels, and David Price (Saturday) and Rick Porcello (Sunday).

Sale leads the majors with 135⅓ innings pitched. He threw 7⅔ shutout innings on Saturday. He’s gone at least seven innings in 15 of his 19 starts.

“After a high-leverage, nearly eight innings of work, we’re going to build an extra day of rest in for him,’’ Farrell said. “So he’ll go out against LA.’’

Starting with Betts

An MVP runner-up who hit 31 homers and drove in 113 runs a year ago might not be the prototypical leadoff hitter.

But Mookie Betts has been at the top of the Sox lineup 65 times this season.

Farrell said it’s a sign of changing approaches to the way lineups are put together across baseball.

“I think over the past probably five, six years, lineup construction has taken a completely different look,’’ Farrell said. “Where so many teams are looking at the No. 3 spot in the order as the most pivotal — that’s your best hitter — a lot of teams now are putting that team in the two-hole.

“I’m sure there’s a lot of debate, a lot of sabermetric approach that goes into your so-called best hitter. The bottom line is you want your guys that get on base the most to get to the plate the most often. So you stack the top of your order the best you can.’’

Betts is tied for third in the American League with 65 runs scored.

A wild swingThere was a scary moment during Josh Donaldson’s at-bat in the first inning. He fouled off a first-pitch fastball from Eduardo Rodriguez. On his back swing, Donaldson’s bat went flying and struck home plate umpire Chris Segal in the head. Segal crumbled to the ground, the rest of the officiating crew came from their spots to check on him. A trainer came from the Sox dugout to tend to Segal. After getting his wits about him, Segal remained in the game.

Lin sent to Pawtucket

After a three-week spark that helped stabilize a third-base position that had been spotty most of the season, Boston’s version of Linsanity came to an end Monday. Utility infielder Tzu-Wei Lin was sent back to Triple A Pawtucket to make room for Rodriguez. In 19 games, Lin hit .280 with two RBIs and a stolen base. Righthander Austin Maddox was also sent to Pawtucket . . . Scituate native Matt Tobin threw out one of the ceremonial first pitches on behalf of the lung cancer-focused nonprofit Lungevity. Last year, Tobin was diagnosed with Stage 4 non-small cell lung cancer, which spread to his lymph nodes and brain.

Julian Benbow can be reached at jbenbow@globe.com.