Higuain ripped a shot that Red Bulls goaltender Luis Robles had not chance to stop.
Frederico Higuain appeared to give Columbus the game winner on a penalty in the 74th minute.
Yeom paid the price when Argentina counter-attacked, and after Messi's shot hit the post Higuain tapped in.
Robles, who had six saves, said watching video of the Crew definitely helped him prepare for Higuain's move.
Striker Gonzalo Higuain volleyed a spectacular equalizer while Kaka put Real 2-1 ahead at the break with a penalty.
CNN: Who needs Messi? Barcelona's big win sends warning to PSG
Gonzalo Higuain had looked to have secured a point for Madrid with an 88th-minute leveller which looked clearly offside.
Liverpool were given a scare when Reina saved a Sergio Ramos header and Gonzalo Higuain put in the rebound.
And the next action saw Bolatti, introduced in the 80th minute for Gonzalo Higuain, finish smartly to seal the win.
Manchester City striker Sergio Aguero restored his side's lead 60 seconds later with Gonazlo Higuain adding a third soon after.
The reward was creating the best early opportunities, with both Higuain and Ronaldo forcing excellent saves from Dortmund's goalkeeper, Roman Weidenfeller.
WSJ: Champions League: Dortmund Holds On to Advance to Final
At Real Madrid, runner-up in La Liga, Karim Benzema and Higuain shared playing time up front, each starting half of Madrid's games.
WSJ: Strikers Likely to Be Focus of Soccer's Summer Transfer Market
Brazil star Kaka also supplied Higuain with the pass for this second of the night and 15th league goal of the season.
Within 90 seconds of the restart, Higuain added the third after excellent work from Kaka, who scored a deserved fourth on 67 minutes.
But Argentina striker Higuain settled nerves with a fine strike before Ronaldo played in Ozil for a second to make it 2-0 at halftime.
Mourinho also brought on striker Karim Benzema and Mesut Ozil for Higuain and Luka Modric, but Real's best chance was ruled out for offside.
Gonzalo Higuain scored a hat-trick for Argentina in what was a comfortable win despite Lee Chung-Yong's goal making it 2-1 just before the break.
Any Argentina nerves, however, were settled when Higuain tapped-in from close range and then he completed his hat-trick by heading home Sergio Aguero's cross.
But they saved their best for last as Messi's stunning chip enabled Sergio Aguero to cross for Higuain to head home to complete his treble.
"I unfortunately couldn't kick the way I'm used to, " Higuain said.
Substitute Gonzalo Higuain added a third after coming on as substitute to all but seal his side's place in the last four with 17 minutes remaining.
Argentina international Gonzalo Higuain opened the scoring on nine minutes as he polished off a swift Real counter attack from fellow countryman Angel Di Maria's cutback.
Ronaldo wrapped it up a minute later from Higuain's low cross, and was booked for tearing off his shirt to pose in front of his adoring fans.
And the winning goal came in the 69th minute when Van der Vaart collected Gonzalo Higuain's pass before firing home a low shot into the bottom corner.
Gonzalo Higuain and Brazilian ace Kaka both scored twice but it was Ronaldo who set Real on the way in the 18th minute with a trademark free kick.
His third goal of the season came seven minutes after Robles went to his right to stop Federico Higuain's penalty after Eddie Gaven was fouled by Brandon Barklage.
Higuain took a stutter step before aiming his shot to the corner in a similar move to the one he successfully employed in the previous match against D.
Barca sits 13 points clear of Real Madrid, which also won 3-0 with two goals from Cristiano Ronaldo and a strike from Gonzalo Higuain seeing off Atheltic Bilbao.
In the 57th minute substitute Mesut Ozil set up Higuain, who later gave Benzema a simple chance in time added on for the Frenchman's eighth in the league.
Higuain's third goal of the season was not without controversy.
Sidney Govou thumped a couple of early volleys past the upright for the hosts while Gonzalo Higuain just failed to control in the box for Real after an excellent move.
应用推荐