But the Scot's comeback lasted just eight minutes as he hobbled off after being on the receiving end of two heavy challenges by Brown, with neither seeing the 33-year-old receive a booking.
"The referee deemed it alright to kick somebody in the shin about four feet off the ground and then it was deemed OK to clatter him again," he said.
"That seems to be OK, that. Just target somebody who comes back from an injury and give him a couple of wallops to see how his leg is coming on."
However, Pompey boss Steve Cotterill leapt to the defence of Brown, claiming he has never advocated targeting players and that Brown was unlikely to know about Thomson's injury.
"I have never, ever targeted a player on his comeback," said Cotterill.
"And I don't think Michael Brown knows Kevin Thomson."