As both teams were looking to break a 1-1 tie, Loyola (12-2-6, 5-0-1 for first place in league) got a crucial break in the final minute of regulation when St. Francis' Sean Fitzpatrick was whistled for tripping up Lucas Gonzalez-Garza on a run into the penalty box.
Justin Jenkins booted home a penalty kick moments later for a 2-1 lead just as the referee announced the beginning of three minutes of extra time.
"I thought the boys played well, I felt bad for them, honestly," Appels said. "That's not the way it should have ended.
"To fight back and get the tying goal and then to give away a penalty on a ball our keeper already had in his hands, it's hard to swallow."
Loyola had led, 1-0, previously on Willie Aviso's goal off a cross from Henry Herrill in the seventh minute.
Just as it had pulled even on a Billy McCreary header when trailing Chaminade in the second half on Thursday, St. Francis (8-8, 4-2) evened the score in the 52nd minute on another header Saturday, this time by Mark Verso.
In the 51st minute, Derek Bell sent a corner kick to Jake La Porte in the middle of the field and La Porte sent a high ball into the goal box where Verso had a header on goal poked out of bounds on a goalie save. On the ensuing corner kick, St. Francis went right back to Verso in the same spot, this time directly off Bell's corner kick and Verso got the result he was looking for.
St. Francis had two more shots on goal down the stretch, including another header by Verso that a Loyola field player smartly deflected with his own head after the keeper had been drawn out of position.
Paul Dean played the entire match in goal for St. Francis and finished with seven saves.
"If we play like this we'll be fine," Appels said. "This is a tough place to play and we have a couple home games coming up with some guys just getting healthy from injury, so I think we're in good position.
"We didn't expect to go undefeated [in league] and I don't expect anybody will."