Would hypnotizing your opponent be against the Yu-Gi-Oh! tournament rules?
From a link on the page that ConMan so helpfully provided:


  Penalties are carried out in the event of rule violations which may cause hindrance to others and/or disruption of the event.
  Please note that the penalties listed on this page is not exhaustive, and the actual penalties enforced may vary depending on severity.   
  
  The Official Tournament Rules &amp; Regulations will be used as a guideline for Judges to determine the penalties to be issued, including its severity. Heavier penalties may be issued for Duelists caught repeating these violations.  
  
  Duel/Match Fixing
  
  Deciding the winner of a match without dueling (e.g. Rock-Paper-Scissors)
  Penalty: Disqualification 
  
  Bribery involving money, cards, or any other means
  Penalty: Total Disqualification


Hypnotizing your opponent would most likely be considered a type of match fixing, leading to a disqualification or a total disqualification.

Additionally, note the verbiage I bolded at the top.  Judges are given broad authority to exercise their own judgement in determining misconduct and applying penalties.  The fact that "there's no rule" against hypnotism would not prevent any competent judge from slapping the misbehaving player with a heavy punishment.

Now, if the judge has been hypnotized too...