The Premier League confirmed the pre-match ritual must take place, guaranteeing an uneasy build-up to the highly-charged west London derby. It will be the first time that Anton Ferdinand and Terry, who has recovered from his ankle injury, will have met on a football pitch since the Chelsea captain's race trial in July.
Terry was found not guilty of using a racial slur against Ferdinand, following an incident in the corresponding fixture last October, but he remains the subject of a Football Association investigation over charges that he denies.
Ferdinand is expected to reject handshakes from Terry and Ashley Cole, who testified as a character witness for his England team-mate at the trial. How many players will emulate Ferdinand in a display of solidarity within QPR's squad is unknown and Hughes indicated they will make their own decision.
"We've had a discussion with the players but that's between myself and them. We don't have to broadcast that," said the QPR manager. "We'll have to wait and see (if Ferdinand shakes Terry's hand). Everybody has a mind of their own and will make a personal decision.
"It's unfortunate that they're in a situation where it's in the public domain. Anton is fine, there's no problem with him."
The rift between Ferdinand and Terry threatens to turn the handshake routine, introduced as part of the Football Association's Respect campaign, into a farce. Should several QPR players also snub Terry or Cole, or both, it could prove embarrassing for the Premier League, who made their decision 24 hours before kick-off.
A Premier League statement read: "There has been dialogue between the Premier League, Queens Park Rangers and Chelsea in relation to tomorrow's match between the two clubs.
"All parties understand and acknowledge that the pre-match handshake will go ahead as part of the normal pre-match activity."
The two teams faced each other in the FA Cup after the controversy erupted last season but the FA chose to scrap the traditional pre-match handshakes due to the sensitivity of the situation. The ceremony was also abandoned before the league match at Stamford Bridge on April 29.
Chelsea manager Roberto Di Matteo said earlier on Friday that his players will go ahead with the handshake.
"They've recovered, had a couple of days training and we expect them to be available," Di Matteo said.
"We're going to respect the rules and the protocol that is in place from the Premier League and set a positive standard to the millions of people watching across the world.
"We'll go ahead with it (the handshake), yes."
Striker Bobby Zamora is one member of the home dressing room who will accept Terry's hand before the game. Zamora told The Sun: "I've known John Terry for years and he's a very good friend of mine. We grew up together and of course I'll shake his hand if he's playing. All this stuff happened a long time before I joined QPR."
Ferdinand’s older brother Rio is also said to be considering snubbing his former England team-mate and centre-half partner Terry when Manchester United face Chelsea on October 28.
Chelsea issued a statement on Thursday afternoon calling for fans to behave themselves.
It said: "Last January's FA Cup match at QPR and the meeting between the sides in April at Stamford Bridge were good examples of passionate and vocal rivalry with the fans of both clubs recognising that abuse and discrimination have no place in a football stadium, nor anywhere else in society.
"Chelsea Football Club wishes to see the level of respect at those games continued throughout this campaign, as it has been in our opening matches.
"Both Chelsea and QPR will work together with the police to ensure that anyone using discriminatory or inflammatory language on Saturday is identified, and that the strongest possible action is taken against them."
The Premier League has not been involved in the ongoing talks between the clubs.
If there is controversy on Saturday it would only be the latest in a number of handshake rows to erupt in the Premier League in recent seasons.
Terry was at the centre of another in February 2010 when his former team-mate Wayne Bridge refused to shake his hand prior to a Premier League game between Manchester City and Chelsea.
Bridge felt aggrieved at allegations in the press that Terry had conducted an affair with his former partner.
Last season, Liverpool striker Luis Suarez was forced to apologise after he refused to shake the hand of Patrice Evra prior to a Premier League game at Old Trafford in February.
Suarez had been found guilty of racially abusing the Manchester United defender.