Jeremy Doku appeared to foul Alexis Mac Allister with a high boot in the penalty area in the last minute of the game.
Speaking in his Daily Mail column, Clattenburg said: "Liverpool should have been awarded a stoppage-time penalty against Manchester City but this is the problem in the Premier League right now referees are making mistakes in matches and not being helped by their VARs."
He added: "Outside of the box, this would have resulted in a free-kick, every day of the week. Just because it happened inside the box does not suddenly transform it into a clean challenge when Mac Allister might be left playing connect the dots on his chest on Monday morning.
"Regardless of the magnitude of the match and the fact it happened in the 98th minute, this was an incident worthy of a penalty."