Terry faces a criminal trial in July from the incident that led to him being stripped of the England captaincy.
Ferdinand was spared having to decide whether to shake Terry's hand before an FA Cup match in January after the Football Association allowed the sides to forgo the traditional ritual.
But the league will not scrap the handshake when Chelsea hosts QPR at Stamford Bridge on April 29.
"It's not a handshake that says everybody loves everybody else," league chief executive Richard Scudamore said Tuesday. "It's a handshake that says, 'For the next 90 minutes, let's just play a game of football.'
"It's nothing more symbolic than that, which is why in our view they should continue. Period."
Liverpool striker Luis Suarez was forced to apologize last month after refusing to shake Patrice Evra's hand in their first meeting since being banned for eight matches for repeatedly directing a racial slur at the Manchester United defender in a match.