Chelsea and former England captain Terry, who denies wrongdoing, has been charged with racially abusing QPR defender Ferdinand in a league game in October.
Terry is due in court in July after the Euro 2012 tournament.
"The Premier League position on the pre-match handshake convention remains consistent. In all normal circumstances it must be observed," the Premier League said in a statement.
"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."
There was no handshake before the FA Cup Fourth Round match in January between the two clubs.
Chelsea, who qualified for the Champions League final on Tuesday at the expense of holders Barcelona despite Terry's first-half red card, can go a point behind fourth-placed Newcastle United with three games left if they win.
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