Konerko was ruled safe and Scioscia came out of the dugout to argue the call -- saying Konerko's running path was in the direct throwing lane of Iannetta, causing the throw to sail wide.
"I know we're filing [a report] with the league and I think it's a very clear case in our favor," Scioscia said. "The umpire set the parameter and told us that Konerko was running well inside the line. All of the umpires agreed with that. The dispute was not, 'Was he running inside the box or outside the box?' They all said he was running well inside the line."
That, according to Scioscia, put Konerko directly in the throwing lane of Iannetta.
"[Second-base umpire and crew chief] Dana Demuth told me that's not the argument," Scioscia said of Konerko possibly being outside the baseline. "He was inside the line, which makes it a virtual impossibility for him not to affect the throw from Iannetta and puts him in the lane of Iannetta trying to throw to first base very clearly. It's quite obvious. They put him there. They said he was inside the line, which puts him in jeopardy, which affects the throwing lane of our catcher. They're the ones who set those parameters. Once they set those parameters, Konerko is out."
The umpiring crew actually huddled twice to discuss the situation before ruling Konerko safe.
"[Ianetta] threw wild, Konerko going down to first was no way interfering with the play at first," DeMuth told The Associated Press. "Konerko no way interfered with the play at first and that was our decision. It doesn't matter where he is running."
Scioscia took issue with the umpires saying they had discretion to rule Konerko out or safe at that point.
"It's a physical impossibility for [Konerko], with the throw coming from home plate to first base, for him not to be in that throwing lane," Scioscia said. "It is physically impossible and that's where the discretion evaporates."
Iannetta had already left the clubhouse before he could be asked about the play, while Pujols declined to comment.
The Angels have 24 hours to file an official report of the contested play with Major League Baseball's department of baseball operations and can expect a ruling within five business days.
The White Sox trailed, 1-0, at the time of the play and tied it on Rios' single to right field in the next at-bat following Konerko -- who then scored on a three-run homer to right by A.J. Pierzynski to make it 4-1 Chicago.
Scioscia said the play then affected the outcome of the game.
"That's why I felt the protest was warranted," Scioscia said. "It's a totally different inning [if Konerko is out]. Everybody goes back. The runners go back to second, it's a double play and you've got first and second, two outs and no runs in ... and it's 15 pitches less that [Zack Greinke] has to throw."
If the Commissioner's Office rules in favor of the Angels, the game would have to be replayed from that point.