The two-time Brownlow Medallist had his left hamstring heavily strapped and did not take to the field in the second half, the injury likely to rule him out of the Saints' Anzac Day eve clash with Port Adelaide next round.
It is the fourth time in the past 12 months that Harvey - who missed seven matches last year - has hurt his hamstrings.
"It's not looking great for him in relation to next week. He couldn't come back on. Whether or not he's hurt some scar tissue we have to wait and found out there," Thomas said.
However, he said Harvey, a veteran of 320 matches, would not let the injury get him down.
"Harvs has been around for 18 years. He knows what it's about and he's had these sorts of adversity before and he'll work doubly hard to come back, whether its next week or he has a couple of weeks off, depending on whether or not he has an injury," Thomas said.
"He's an enormously resilient person; he's been probably one of our best performers so far this year so I'm sure he'll bounce back."
Had Harvey not been hurt, the Saints could have entered their round four clash with the Power at AAMI Stadium at full strength, with the 11-day break between matches likely to allow star pair Luke Ball and Justin Koschitzke to return from injury.
"That's what footy's about. It's about trying to work towards getting to your best side all the time," said Thomas.
"It will happen for us. Hopefully it does later in the year."
However, Thomas was pleased with the Saints' performance against the Lions, describing the game as their best performance of the year.
"We've been very good with our pressure skills. One of our measurements - selfless acts - this year has been terrific for the three games but when we've had the footy we haven't been able to complete and we've been a bit rusty," he said.
"Our key forwards have got to work much more closely together and when we do that, when we isolate and move the ball very quickly through the middle, we're an imposing team."
"But like anyone if we're just a little bit off our tucker and our confidence isn't there and we're taking the ball in haphazardly, we're susceptible to a strong defence when they've got extra numbers behind the footy."
