Chelsea skipper Terry is accused of racially abusing QPR's Ferdinand during a match at Loftus Road in October.
He denies the accusation but faces a court case, which starts on 9 July after Euro 2012.
Ferdinand's lawyers had told him not to shake Terry's hand for fear that it could prejudice the forthcoming trial.
"The Premier League position on the pre-match handshake convention remains consistent," said a Premier League statement. "In all normal circumstances it must be observed.
"However, after discussions with both Chelsea and Queens Park Rangers about the potential and specific legal context in relation to John Terry and Anton Ferdinand, the decision has been taken to suspend the handshake convention for Sunday's match."
•23 Oct 2011 - QPR beat Chelsea 1-0 in bad-tempered match
•26 Oct 2011 - FA begins investigation. Terry vows to clear name
•31 Oct 2011 - Ferdinand says he has "strong feelings" on case but won't comment until after FA investigation
•1 Nov 2011 - Metropolitan Police begin formal investigation after assessing evidence
•3 Feb 2012 - Terry stripped of England captaincy after Crown Prosecution Service decides he should stand trial in July over allegations
When the clubs met in the fourth round of the FA Cup in January the pre-match handshake was cancelled.