Raphina's goal and assist was the difference at St James' Park despite a rejuvenated second-half performance from Newcastle United.
A quick response to Miguel Almiron's goal from Jack Harrison was enough to secure a vital three points for Leeds United in a game of two contrasting halves.
Story of the game
Leeds opened the scoring through Raphina after 16 minutes with a finish into the bottom corner.
Almiron levelled it up after a nice one-two with Callum Wilson just before the hour mark.
Leeds responded instantly as Jack Harrison fired in from a tight angle three minutes after Newcastle scored.
After a slow start to the half with a number of players going down injured, it was Harrison with the first chance in the 11th minute but his volley ended up behind the winger after slicing it.
Leeds were constantly attacking the wide areas and after Ezgjan Alioski stole the ball they had five players running at the Newcastle goal. Rodrigo had time to turn and get his head up before cutting it back to Raphina on the penalty spot and he curled it past Karl Darlow.
Newcastle almost responded instantly after not creating anything before the goal as Jamaal Lascelles rose highest to head Jonjo Shelvey's corner blasting past the far post.
Ryan Fraser showed what he was capable of as he whipped in a delightful ball which Illan Meslier came for at the last second which saw him get clattered in the face by Jacob Murphy's knee as the winger missed the ball.
A Big chance squandered for Fraser after Newcastle began to put some pressure on Leeds and they won the ball in the away sides final third before murphy fired it across to Fraser arriving into the box late but his shot zipped over the bar.
Leeds almost doubled their lead on half time through one long ball which released Rodrigo who put two defenders on the floor before seeing his effort saved by Darlow.
The Spaniard recovered the ball and set Raphina away to the byline but his chipped effort cannoned back off the post.
Seconds later Rodrigo was causing problems again as he cut onto his left foot on the edge of the box and firing an effort drilled to the bottom corner but it skidded narrowly wide of Darlow's post.
Minutes into the second half and Leeds had the ball in Darlow's net again but after Stuart Dallas' initial effort was blocked, the rebound hit his arm and looped into the top corner and was quickly ruled out.
Newcastle won a free-kick on the corner of Leeds' box and Shelvey curled it onto Lascelles' head but the defender again could only fire his effort wide of the post.
The Magpies had pushed much higher up the pitch to pressure Leeds in the second-half and they got their reward as Almiron ran at the heart of the defence and exchanged a pass with Wilson.
The Paraguayan took one touch before slotting it beneath Meslier who got a glove on it.
Raphina picked up the ball on the left before delivering an inch-perfect pass to Harrison who only needed one touch before firing a half volley past Darlow and in off the post.
Leeds had drawn Newcastle onto them and launched an electric counter-attack with Raphina at the heart of it, like every good move they put together.
The game was extremely open in the second-half as only five minutes after going behind Jamal Lewis found himself played through but he took a touch and snapped at his effort which hit the bar when he should've done much better to trouble Meslier.
Newcastle should've been level as Lascelles, again, got on the end of a Shelvey set-piece but this time it was on target and required Meslier to tip it onto the bar and out for another corner.
The introduction of Allan Saint-Maximin changed the tempo of this game as he was driving forward with every opportunity and penning Leeds back to their own box.
It was Shelvey's turn to turn to get on the end of a set-piece as Fraser put a corner n the six-yard box and either side of Meslier the midfielder scores but it's down the keepers' throat and pushed it over the bar.
Fabian Schar almost got Newcastle back level after a mazy run from the halfway line saw him eventually curl one from the edge of the box which required a strong hand from Meslier to keep it out.
Saint-Maximin is so important to Newcastle
Before the Frenchman was introduced in the second-half Newcastle looked clueless in the final third. However, as soon as he entered the game he drove the Magpies forward.
He was looking to go forward and make something happen every time he got the ball and he was forcing the Leeds defenders closer to their goal.
On numerous occasions, he drew two/three players to the ball which left a teammate wide open, like for Lewis' effort which hit the bar.
If Steve Bruce is to stay in a job and Newcastle are to maintain their Premier League status, Saint-Maximin will have to keep himself fit and firing on all cylinders.
A much-improved second-half but another defeat piles on the pressure
While Bruce will be encouraged and impressed with how his side performed in the second-half he knows the only thing that matters is results.
It's now 11 games without a win for Newcastle with teams below them guaranteed to pick up points this week and Bruce needs his side to be more composed in front of goal as they squandered a number of glorious chances to pull themselves back into the game.