The incident in question occurred in the first minute of the game and Rowntree, the Lions' veteran prop, will now appear before an independent judiciary hearing.
Meanwhile, Auckland centre Sam Tuitupou has been cited for "allegedly stamping or trampling" on Gordon D'Arcy in the 52nd minute of the game.
Rowntree was cited by the International Rugby Board's independent commissioner Dennis Wheelahan QC of Australia after the game.
The disciplinary hearing will be conducted at Eden Park by the IRB's judicial officer Terry Willis - the same official who suspended Danny Grewcock for two months after the Lions lock was found guilty of biting Keven Mealamu in the first Test.
Rowntree's involvement in the final midweek game indicates he will not be involved in Saturday's third Test, with Andrew Sheridan set to feature against the All Blacks.
Any suspension would confirm the 34-year-old as unavailable for the Test but it would have to be extremely severe to run into the start of the new Guinness Premiership season, which for Leicester begins on September 3 at home to Northampton.
Tuitupou can consider himself fortunate not to have been cited on two counts after his punch on Ben Kay left the Lions lock nursing a gruesome black eye and forced him from the field.
But Tuitupou did not escape the citing commissioner's attentions entirely and he must also front up to Willis.