Jose Reyes singled home the winning run in the 10th inning as Toronto beat Tampa Bay 5-4. Maddon, however, said afterward that he felt his grievance was "pretty cut and dried."
"I'd be really surprised if the protest is not upheld," Maddon said.
Rays designated hitter Wil Myers reached on a one-out single in the fourth and was called safe by first base umpire Bill Welke on Mark Buehrle's pickoff throw.
After Yunel Escobar stepped back into the batter's box and Buehrle returned to the rubber, Blue Jays manager John Gibbons came out and asked to challenge Welke's call.
Maddon came out to speak with crew chief and third base umpire Bob Davidson about the timing of the challenge. After Myers was called out following video review, Maddon spoke to Davidson again and indicated he was playing the game under protest.
"It was inappropriate for Bob to do what he did and permit that to happen," Maddon said. "I'm trusting that they're going to interpret the rule properly and get us back to that point in the game."
Davidson told a pool reporter that he saw Gibbons emerging from the dugout just as Escobar was stepping back into the box.
"(Escobar) was just about getting in, but I'm looking at Gibbons and he's coming out and he's not a speed merchant, and I thought, it's on time," Davidson said. "We want to get the play correct. That's what we're out here for."
Baseball's replay rules say any challenge must be made before the next play or pitch, which is said to begin "when the pitcher is on the rubber preparing to start his delivery and the batter has entered the batter's box." The rules also say, however, that the crew chief has "the final authority to determine whether a manager's challenge is timely."
The San Francisco Giants on Wednesday became the first team since 1986 to win a protest after Major League Baseball ruled that the tarp at Wrigley Field had not been properly put away after its previous use. The Giants were able to resume Tuesday's rain-shortened game that the Cubs thought they had won 2-0, eventually beating Chicago 2-1 on Thursday afternoon.