Unruly spectators jeered club officials and set off a succession of flares as Glory crashed to a 3-0 loss at home to Sydney FC on Friday, hours after the FFA issued the punishment for salary cap breaches.
A 13-year-old boy was taken to hospital after suffering burns to his legs from a flare, local media reported on Saturday.
"They're going to be disappointed. They've worked ever so hard to get into a fantastic position," Lowe told local media of his players.
"But we're professionals. We get paid to do a job. As hard as it is, that's what we're going to do for the next two games.
"You're disappointed, but you can't let yourself down. Everyone is in this together.
"We'll probably feel a bit sorry for ourselves in the next day or two.
"But we've got two days off, we'll come back into training, and bang back at it again."
Though lying third on the 10-team table with two rounds to play, Glory will be automatically relegated to seventh at the end of the regular season.
The FFA said it had found the club had failed to disclose payments and benefits to at least six players and exceeded the salary cap by around A$400,000 ($307,000) for the current season.
Glory management were defiant, however, and have applied to Western Australia's Supreme Court seeking an injunction against the FFA verdict.
Glory chief executive Jason Brewer said the players' payments were "forecast" to be under the salary cap of A$2.55 million in the current season.
"We go into the next games on the basis that for all Perth Glory fans out there, our players are playing for points," he said.
Police had charged two teenagers with setting off the flare that injured the boy and the venue manager said it would slap five-year bans on unruly fans.
Security would also be boosted for Glory's match against Melbourne City on Friday.
"Other patrons who displayed disorderly or inappropriate behaviour will also face lengthy bans,” News Ltd media quoted a statement by VenuesWest chief executive David Etherton as saying.
($1 = 1.3028 Australian dollars)
(Writing by Ian Ransom; Editing by Greg Stutchbury/Amlan Chakraborty)
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