The Ravens improved to 4-4 with to maintain pressure on Pittsburgh in the AFC East but the game was overshadowed by the ugly incident that ended Flacco's participation in the game towards the end of the second quarter.
The 32-year-old Super Bowl-winner was clearly sliding after a nine-yard scramble on third down near Miami territory when Dolphins linebacker Kiko Alonso slammed into him with a wild shoulder charge.
The blow sent Flacco's helmet flying and triggered a melee involving players of both sides.
A groggy Flacco was taken to the sidelines with concussion and played no further part in the contest. Video footage showed Flacco bleeding from his ear as a result.
Although Alonso was penalised for unnecessary roughness, he was not ejected from the field following the hit.
Ravens coach John Harbaugh reacted furiously to Alonso's head-shot, but later refused to be drawn on whether he thought the Miami player should face a suspension.
"I'm not commenting on that," Harbaugh said. "It was penalised correctly."
The National Football League had vowed to crack down on dangerous shots to the head before the season, following mounting concern over the issue of concussions and head trauma in the sport.
Flacco's absence did not disrupt a one-sided Ravens win, with backup Ryan Mallett coming in to set up Ben Watson for a two-yard touchdown to put Baltimore 20-0 up at halftime.
Miami then imploded in the fourth quarter, with quarterback Matt Moore giving a nightmare performance.
Moore then telegraphed another interception for the rampant Ravens defense, with Jimmy Smith running 50 yards to the end zone for the score.
The Dolphins will now wait to see if Alonso is issued with a further sanction following his hit on Flacco.
Dolphins star Ndamukong Suh could also face disciplinary action after receiving two unnecessary roughness penalties. Suh, who has a chequered disciplinary record, was seen shoving Ravens back-up Mallett in a fourth-quarter scuffle.