Thomson was reported by independent International Rugby Board citing commissioner, Ireland's Murray Whyte, following the 43rd-minute incident.
A statement issued by Six Nations organisers, who oversee autumn Test disciplinary matters, said Thomson would face a disciplinary hearing in London on Wednesday.
Thomson was sent to the sin-bin by referee Jerome Garces on advice from touch judge Simon McDowell.
Television replays showed that Thomson brought his boot down on Strokosch's head, suggesting he was fortunate to escape with only a yellow card.
New Zealand cruised to a 51-22 victory, but Thomson now faces a ban that could rule him out of the world champions' remaining autumn Tests against Italy next Saturday, followed by Wales and then England.
Asked after the game if it should have been a straight red card awarded to Thomson, Scotland head coach Andy Robinson said: "You would think so."
If he is suspended, then it is likely that Thomson could be sidelined for anything between three and eight weeks.
Australia lock Rob Simmons, meanwhile, will also appear before an independent IRB judicial officer on Wednesday.
Simmons was cited by South African Freek Burger for a dangerous "tip" tackle on France flanker Yannick Nyanga midway through the second half of Australia's 33-6 defeat against Les Bleus in Paris on Saturday.
Australia face England at Twickenham next Saturday.