A 1-0 victory for Barca at fourth-placed Real Mallorca on Saturday put the champions three clear but Real responded to draw level on 74 points with their arch-rivals and reclaim top spot on goal difference.
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Atletico, who have not won a Madrid derby in more than 10 years, led 1-0 at the break thanks to a curled effort from former Real player Jose Antonio Reyes, before Alonso, Arbeloa and Gonzalo Higuain struck to put the hosts 3-1 ahead.
Diego Forlan pulled one back from the penalty spot with just over 20 minutes left after Alonso handled at a corner but Real comfortably held on to claim the three points.
With nine matches remaining, the top two are 21 points ahead of third-placed Valencia and Real host Barca in the potentially decisive "Clasico" in two weeks.
The home fans unfurled an enormous banner shortly before kickoff at the Bernabeu showing a collection of Real ghouls standing menacingly over a young Atletico supporter cowering in bed and the slogan in giant letters: "Your worst nightmare".
The match initially looked liked turning into a bad dream for the hosts thanks to Reyes, who helped Real win the title with two goals on the final day of the 2006/07 season while on loan from Arsenal.
DELICATE SHOT
Portugal midfielder Tiago drove toward the penalty area and fed Sergio Aguero, who flicked the ball wide to Reyes to curl a delicate shot past Iker Casillas into the corner of the net.
The best first-half chance for a Real equaliser fell to Cristiano Ronaldo. Alonso floated a cross into the area and the unmarked Portuguese forward, usually so effective in the air, somehow failed to net his header with only keeper David De Gea to beat.
Real continued to pile on the pressure after the break and Alonso put them level in the 49th with a close-range header.
The midfielder's cross-field pass sent Arbeloa clear to put Real in front six minutes later and a defensive lapse let Higuain in for a third in the 62nd, the Argentina forward's 23rd of the season.
An attempted Tiago clearance hit team mate Paulo Assuncao and Higuain stroked the ball past De Gea to close within two of top scorer Lionel Messi.
Alonso inexplicably threw up an arm to give away the penalty in the 68th and Forlan gave Casillas no chance with a powerful low drive.
Real have now won all 15 of their home matches this season and it was their 11th straight league win.
TROUBLED SEASON
Sevilla's troubled season took a turn for the worse when they crashed to a 3-0 defeat at Villarreal in new coach Antonio Alvarez's first match in charge.
Manolo Jimenez was sacked after Tuesday's draw with basement side Xerez and Sevilla have now
