Jason Jaffray and Yannick Tremblay each added a goal and an assist for Manitoba (10-8-3-2) and Lee Goren notched two assists.
Gino Pisellini had the only goal for Philadelphia (8-11-1-0), while goalie Scott Munroe stopped 31 of 34 shots.
With Manitoba trailing 1-0 in the first period, Jaffray tied the score at 10:24 with his 14th goal of the season after his shot deflected off Philadelphia's Nate Guenin.
Moran then gave Manitoba a 2-1 lead at the 13:52 mark when he jabbed a loose puck out of the reach of Munroe and into the net for his 10th of the season. Flaherty, in his third season with Manitoba, preserved the lead for the Moose, who were outshot 16-6 after one period.
The 38-year-old netminder made a key save midway through a scoreless second period when he stopped a redirection attempt by Mark Cullen on a 2-on-1 shorthanded break.
Tremblay completed the scoring at 14:35 of the third period with the Moose on the power play after he one-timed a pass from Moran for his third of the season. Manitoba outshot Philadelphia by a 28-13 margin over the final two periods.
Pisellini opened the scoring at 4:33 of the first period with his first of the season after putting in a loose puck from a sharp angle to give the Phantoms a 1-0 lead. Philadelphia controlled play during the first ten minutes of the contest, outshooting Manitoba by an 8-1 margin.
The Moose travel to Hershey on Saturday to take on the Bears before returning to Philadelphia on Sunday to play the Phantoms again.