QPR's first win in the topflight at Stamford Bridge since March 1979 was secured by Shaun Wright-Phillips scoring against his former club.
The end of Chelsea's four-game winning run in one of the biggest shocks so far this season left Benitez's side fourth in the standings, 14 points behind leader Manchester United.
"Maybe in odd areas we were tired," Benitez said. "You could see we didn't have the intensity and the pace on the pass and the movement that we were expecting."
Everton is only two points behind after beating Newcastle 2-1, but has played a game more than both Chelsea and sixth-place Arsenal.
Liverpool still has its sights on the top four, beating Sunderland 3-0 to move seven points behind Chelsea but having played a match more.
Benitez's decision to make five changes from the Chelsea side that beat Everton at the weekend appeared to backfire, with Chelsea struggling to impose itself with midfielders Eden Hazard and Juan Mata, and defender Ashley Cole among those watching from the bench.
"We cannot carry on with the same players every game," Benitez said. "If you are playing a team that is bottom of the table at home you have to trust your players."
One of the players handed an unexpected first league start, Marko Marin, was fortunate to last beyond the fourth minute after only receiving a yellow card for a studs-up challenge over the ball and into Stephane Mbia's shin.
QPR's breakthrough came when David Luiz only half-cleared a corner in the 78th minute, and Adel Taarabt teed up Wright-Phillips to smash the ball into the net of the team he left in 2008.
QPR remains at the bottom but is now only behind Reading on goal difference, although the team remains eight points from safety.
"I can't remember having many better wins than this," QPR manager Harry Redknapp said. "Chelsea are absolutely flying at the moment and, on the back of our defeats against Liverpool and West Brom, it was a great result for us."
Ahead of the match, Chelsea was closing in on a deal to bolster its striking options by signing Demba Ba from Newcastle after offloading Daniel Sturridge to Liverpool.
Sturridge watched his new side sweep to a comprehensive victory over Sunderland, with Luis Suarez taking his league tally to 15 goals this season with a double after setting up Raheem Sterling's opener.
Suarez buried his first in the net in the 26th and was on target again at the start of the second half after being released by Steven Gerrard.
Despite Sturridge's arrival, Liverpool manager Brendan Rodgers will find it hard to rest Suarez.
"He is a Lionel Messi-type character in terms of he is angry when I give him a breather," Rodgers said. "At the start of the season I tried to rest him and he didn't want it.
"He is a player that to be at his top of his game has to play two or three times a week, one game is not enough. He needs to be playing and you see the response you get from him."
The result left Sunderland four points above the relegation zone, but two points higher than northeast rival Newcastle.
Papiss Cisse headed Newcastle in front after only 72 seconds, but Leighton Baines levelled with a powerful free kick before halftime and Victor Anichebe tapped in the winner on the hour.
Newcastle has now lost three consecutive games, having also gone down 7-3 to Arsenal and 4-3 to leader Manchester United.
"We have had an awful run, but I thought tonight we gave a really honest account and we can't ask for more than that from the players we had on the pitch," Newcastle manager Alan Pardew said. "But in the end, Everton had a bit more guile, a bit more experience and a bit more quality, and that's what we need to bring back."
Newcastle is preparing for life without Ba, who has scored 13 goals this season before entering into transfer talks Wednesday with Chelsea.
"There is a positive because if he had gone with two days to go of the window and we hadn't got a replacement in, suddenly we are in real trouble," Pardew said. "We have got time and hopefully that will work in our favour."