Stoll's tally on a feed from Muzzin midway through the first period handed the Kings a 2-0 lead and Los Angeles went on take its ninth victory in 11 contests.
Muzzin also helped out on Dustin Brown's power-play goal as the Kings swept their season's series from Calgary for the first time since the 1999-2000 season.
Jonathan Quick turned aside 23-of-24 shots to record the win.
Mikael Backlund scored in the final frame for the Flames, who lost their third straight.
Joey MacDonald made 19 saves for Calgary.