The Football Association gave the clubs permission not to undertake the usual handshake routine prior to Saturday's FA Cup fourth-round tie at Loftus Road.
That spared Anton Ferdinand having to shake the hand of Chelsea captain Terry, who has been charged with racially abusing his fellow defender and faces a court case that begins on Wednesday.
Ferdinand was reportedly agonising over whether to ignore Terry - who denies the allegation against him - ahead of what was their first meeting since their altercation during October's Barclays Premier League game.
Rangers boss Hughes revealed he held a meeting with his players at which some of them suggested they would be prepared to join Ferdinand in snubbing Terry.
"There could well have been an issue but players make their own decisions," Hughes said.
"I said Anton was the guy who had to make his own decisions for himself about whether or not he shook John Terry's hand.
"With the group I have got I know they wanted to support their team-mate and the situation in the end was to take it out of the equation and not to have the issue."
He added: "There were discussions this morning as well and Chelsea had their views and basically we all came to the same decision."
Blues manager Andre Villas-Boas knew nothing of suggestions more than one QPR player would snub Terry and revealed he only learnt there would be no handshakes 45 minutes before kick-off.
But despite insisting it was "extremely important" Ferdinand and Terry shook hands, Villas-Boas said: "It was a wise decision bearing in mind the expectancy that was aroused from the fact that a couple of events could happen in that handshake.
"It was wise not to do it because it could have an impact on crowd behaviour."
The handshake issue is likely to arise again when the sides meet at Stamford Bridge in the league in April.
Hughes called for the entire ritual to be dropped, saying: "I think they are an irritation. I don't know where they have come from, who dreamt it up, why people think it is vitally important that teams do this.
"There is nothing wrong with what happened in the good old days when I played and you ran out and played a game of football, which happened today."
Villas-Boas disagreed, saying of Saturday's abandonment: "I think it was decision for the moment."
Both managers praised their respective players for their performances, with neither Terry nor Ferdinand putting a foot wrong.
Villas-Boas said: "Individually from John, it was an excellent performance, very, very focused, managed to get the off-the-field events out of his mind and concentrate on his job."
Hughes added of Ferdinand, who allegedly received a 'pellet' through the post this week: "It was difficult for him as the focus seemed to all be on Anton, which is understandable given what has happened in the last 48 hours."
Terry was mercilessly jeered and abusively taunted but Hughes did not feel this acted as motivation for the defender.
"John is a big figure in the game and I am sure he gets booed at every away game," he said.
"I think he plays the same way and rarely have I seen anything created by headlines effect John Terry, which was the same today.
"For him to come through that, I think shows great credit.
"He was of the mind he was going to play today and he put in a great performance."
Chelsea's fans refrained from the infamous "Anton Ferdinand, you know what you are" chant, but a QPR supporter could be in trouble after a steward alerted referee Mike Dean's attention to the match ball being thrown from the crowd and hitting the back of Ashley Cole.
Dean had a good game but arguably made a mistake awarding the penalty which handed Chelsea their 1-0 win after adjudging Clint Hill to have pushed over Daniel Sturridge.
Hughes said: "I think Mike Dean will be a little disappointed when he sees what decision he has given.
"I just felt Daniel Sturridge went down a little bit easily."
Villas-Boas, whose side lost 1-0 at Loftus Road in October to a soft penalty, said: "It's very similar to David Luiz and (Heidar) Helguson here and nobody seemed to criticise anything.
"We finished the game for the league here with nine men and (were) maybe treated unfairly.
"Maybe QPR this time got treated unfairly."
Chelsea lost Ramires to a medial ligament injury that could rule out the midfielder for a month, while Helguson suffered a groin problem that looks set to keep him out of QPR's game at Aston Villa on Wednesday.