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Walters had a nightmare afternoon at the Britannia stadium, putting through his own net with a diving header on the stroke of halftime, then beating Stoke keeper Asmir Begovic again with a header from a corner just past the hour. He also missed a late penalty.
Stoke have not beaten Chelsea in the league since 1975 and Frank Lampard's penalty and a fine Eden Hazard goal put the Londoners one point ahead of fourth-placed Tottenham Hotspur who drew 0-0 at Queens Park Rangers in the lunchtime kickoff.
Rangers prop up the standings after Reading staged a remarkable comeback to beat West Bromwich Albion 3-2, scoring three times in the last eight minutes after trailing to Romelu Lukaku's double.
Aston Villa dropped into the bottom three following Southampton striker Rickie Lambert's contentious first-half penalty that secured their fellow strugglers a 1-0 victory at Villa Park.
Leaders Manchester United host fierce rivals Liverpool on Monday before second-placed Manchester City, seven points behind Alex Ferguson's side, complete the weekend programme at Arsenal.
Chelsea moved within four points of City, and 11 behind United, after getting a helping hand - or head - at Stoke, normally ferocious opponents on home turf.
Victory should bring some relief to Benitez amid growing discontent among Chelsea fans still seething at the Spaniard's appointment and his team's inconsistent performances.
In their previous two games Chelsea suffered a shock home league defeat by QPR followed by a midweek loss to Swansea City in the first leg of the Capital One (League) Cup semi-final at Stamford Bridge.
Chelsea also got a boost on Saturday with the return to first-team action of captain John Terry after two months out with a knee injury.
Terry replaced Juan Mata after 79 minutes although he did concede the late penalty which the hapless Walters struck against the top of the bar.
Reading gave their fans hope that they can stay up with an unlikely win over West Brom at the Madjeski stadium.
Until the 82nd minute they had been run ragged by on-loan striker Lukaku but Jimmy Kebe started a memorable comeback. Adam Le Fondre then equalised from the penalty spot with two minutes to go before Pavel Pogrebnyak pounced in the last minute.
"We were really resilient. We have got great character," Reading manager Brian McDermott told Sky Sports.
The main talking point at Villa Park surrounded Lambert's 34th minute penalty that earned Southampton the three points. Enda Stevens was penalised for bringing down Jay Rodriguez and both managers agreed the decision was harsh.
"Enda Stevens was not even close to him and that is the most hurtful thing. I think referee Mark Halsey will be embarrassed by that," said Villa boss Paul Lambert.
His opposite number Nigel Adkins agreed, stating: "For me there is no contact with the player but the referee has a decision to make.
"All we can do at our place is make sure the players are not diving. We expect the players to behave properly, it is not a dive from Jay Rodriguez, there was no contact, but if the player had not moved his leg away, there would have been contact."
Goalscorer Lambert took a different view. He said it was a "stonewall" spot-kick.
QPR manager Harry Redknapp had to be content with a point in his first game against his former club Tottenham Hotspur.
Redknapp, sacked by Spurs in June, hailed a "fantastic" performance from his side as they stifled their opponents for long periods.
In other matches, fifth-placed Everton and Swansea battled to a goalless draw at Goodison Park, as did Norwich City and Newcastle United at Carrow Road while Sunderland thumped West Ham United 3-0 at the Stadium of Light.
Fulham drew 1-1 at home to Wigan with Franco Di Santo's equaliser lifting the visitors out of the relegation places, ahead of Aston Villa on goal difference.