Calgary had the second-best power play in the league at home last season and it showed flashes of that prowess in the second period, connecting twice with the extra man to open up a 2-0 lead.
It was the first goal of the preseason for the 6-foot-5 defenseman, who joined the Flames last November in a trade with the Carolina Hurricanes.
Babchuk, 27, became an unrestricted free agent on July 1 but re-signed with Calgary just three days later, agreeing to a $5 million, two-year contract.
Glencross also scored for Calgary (3-3) while Jokinen had two assists. The Flames are now off for eight days before opening the regular season at home next Saturday against the Pittsburgh Penguins.
Kiprusoff, who played his first full game, ended up with 21 saves. He was at his best in the first period turning aside all nine Phoenix shots to keep the game scoreless despite the Coyotes 9-6 edge in shots.
Two of the shots came off a chance by Patrick O'Sullivan, who was denied twice at the side of the net by the veteran Flames goaltender.
The Coyotes wrap up their preseason schedule Saturday night at home against the San Jose Sharks.
Tanguay was given the night off while Iginla continues to recover from back spasms, which has sidelined him most of training camp. The Flames' captain did skate for 20 minutes earlier in the day, his first time back on the ice since leaving practice early on Sept. 17.
Calgary's penalty killers also had a superb second period, killing off a 1:47 two-man advantage.
Jokinen set up Glencross's second goal in as many games at 16:03 of the third to make it 3-0, then Gordon responded 12 seconds later to get the Coyotes on the board.
Whitney added his second of the preseason at 17:51, but Moss put the game away with an empty-netter with 42 seconds remaining.