The 40th-minute glancing header edged Raul closer to Alfredo di Stefano's all-time record of 214 Liga goals, while the Madrid native is now two shy of the same man's tally of 307 in all competitions.
The winning touch came from a quickly-taken set piece, as recent signing Lassana Diarra swung over an excellent left-wing cross that Raul flicked past Gustavo Munua with his right ear.
It was a fiercely-contested match, with the competitiveness spilling over on several occasions.
Depor midfielder Lafita was incredibly fortunate to stay on the pitch when he launched into a high, late and dangerous tackle that could have snapped Fernando Gago's standing leg, one of several rough challenges from both sides.
New coach Juande Ramos lost his first match in charge 2-0 at Barcelona, but his side have since taken maximum points domestically and have only conceded once in five matches.
They hedged their bets though, as the visitors were impressive both in attack and defence.
Depor were unlucky not to score when left-back Filipe hit the top of the bar with a long-range shot, while Iker Casillas made a spectacular save from Lafita.
Madrid, meanwhile, looked at their most dangerous on the counter-attack with the reborn Arjen Robben marauding on both flanks.
The Dutchman is in the form of his life and created chances for Gonzalo Higuain, Raul, Wesley Sniejder and Rafael van der Vaart and almost scored himself with a superb solo run at the end that was foiled by Munua in the Depor goal.
Miguel Angel Lotina's side welcomed back playmaker Juan Carlos Valeron, who started for the first time in 18 months after a three-year injury hell that almost saw him retire.
Valeron, 33, looked every bit the player he was in the early part of the Noughties, with some deft touches and crafty passing, and although he tired towards the end his return will be a big boost to Depor, who themselves are back in the top half of the table after a difficult few seasons.
Madrid stay second after the win but are still 12 points behind leaders Barcelona, while Deportivo remain eighth.
Sevilla 0 Racing Santander 2
Sevilla spurned the chance to go second in La Liga when they slumped to a 2-0 home defeat to Racing Santander despite the visitors being down to 10 men for an hour of the match.
The hosts went 1-0 down when defender Cesar Navas's struck from close-range after Nikola Zigic rose to head a Pedro Munitis free-kick against the crossbar.
Oscar Serrano was harshly shown a straight red card just after the half-hour mark for a trip on Adriano.
But Manuel Jimenez's side failed to take advantage and conceded one minute after the second-half restart when Frederic Kanoute diverted a Munitis free-kick past his own goalkeeper Andres Palop.
Sevilla dominated possession in the second half but were unable to create enough clear-cut openings.
When they did have chances, Diego Capel and Luis Fabiano fluffed their lines, while Tono made a great save from Finnish substitute Teemu Pukki.
The defeat leaves Sevilla in third, while Racing move up to ninth.
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Mallorca 3 Valencia 1
Mallorca were led to their first league victory since late October by midfielder Jurado.
The 22-year-old pounced on a loose ball for the first after eight minutes and was brought down for a penalty which Jose Luis Marti scored in the 41st.
A minute later, Jurado broke away for the third.
Vicente pulled one back for Valencia in the second half.
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Almeria 2 Athletic Bilbao 1
Hugo Sanchez's second league win at the helm of Almeria was sealed with two first-half goals.
Juanma Ortiz headed the opener after 26 minutes and Kalu Uche swivelled to score the second before the break. Joseba del Olmo broke away to score for the visitors midway through the second half.
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Getafe 5 Sporting Gijon 1
Sporting's new signing Inaki Lafuente had a debut to forget in goal as Getafe ended a run of four straight defeats in style.
Striker Roberto Soldado made the most of an error to score Getafe's opener, and Esteban Granero looped in a shot from distance soon after.
David Barral's solo effort put Sporting back in the game just before the break but Soldado scored again, Ikechukwu Uche made it 4-1, and Soldado completed his hat-trick from the penalty spot.
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Malaga 1 Atletico Madrid 1
Atletico are still seeking their first win of 2009 after coming from behind to draw with the team just below them in the standings.
Apono's long-range shot skimmed off a defender to put Malaga ahead in the 22nd minute, but John Heitinga levelled at a free-kick just before halftime.
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Valladolid 1 Espanyol 0
New Espanyol coach Mauricio Pochettino was unable to crown his league debut at the helm with a victory.
Valladolid's Henok Goitom nudged in Jonathan Sesma's shot after 42 minutes, but Sergio Sanchez levelled with a header from a corner 11 minutes from time.
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Recreativo 1 Real Betis 0
Recre's mini-revival continued with a fourth game unbeaten at the expense of Andalucian rivals Betis.
Javier Camunas scored the winner 18 minutes from time with a superb glancing header.
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