With two outs, Molina's one-hop hit appeared to bounce off a sign above the left-field wall and carom back into play. Matt Carpenter was able to score from first for the winning run.
Reds manager Bryan Price ran after the umpires, who left the field as soon as Carpenter touched the plate.
The Cardinals began the day one game behind San Francisco for the second NL wild-card spot.
The rule states that a team must show an intent to challenge within 10 seconds and to actually challenge within 30 seconds of the disputed call.
According to reporter Derrick Goold of the St. Louis Post-Dispatch, the rule at the end of a game is for an "immediate" challenge by the team. The "10/30" rule therefore did not apply in this case.
The Associated Press contributed to this report.