Jozy Altidore, playing just his third match with the U.S. national team and his first in the run-on side, scored in the 40th minute, only to have Magallon draw even again in the 47th.
Onyewu also scored for the Americans, who twice blew leads but extended their home unbeaten streak against Mexico to 10 matches while outscoring their southern neighbors 17-3.
The match, played four months before the teams start qualifying for the 2010 World Cup, drew 70,103 boisterous fans, most of them clad in green and cheering for El Tri.
Mexico controlled the ball most of the match and outshot the Americans 13-3, testing U.S. goalkeeper Tim Howard.
The fast-paced game was marked by physical play with the United States called for 19 fouls and Mexico whistled for 13.
Onyewu made a throw-in that led to the first goal when Landon Donovan controlled the long pass over his shoulder, spun and popped the ball back toward the 1.93-meter (6-foot-4) Onyewu, who outleaped defender Israel Castro and headed the ball past goalkeeper Guillermo Ochoa on an angled shot from about 8 meters that went in off a post.
Mexico tied the game on a restart from just outside the penalty area. Pavel Pardo hooked a pass toward the far post and Magallon booted it home as defender Drew Moor grabbed his jersey from behind. The 26-year-old Magallon scored his first goal in 20 international matches.
The Americans retook the lead when Altidore, a rising 18-year-old star for Major League Soccer's New York Red Bulls, headed a long pass from Moor past a frozen Ochoa.
Clint Dempsey appeared to score another U.S. goal late in the half, but it was called back for offside.
Carlos Vela missed a left-footed shot wide of the net in the opening minute of the second half. The Mexicans kept the attack at the American end and tied the game on a corner kick that ended with Magallon beating Moor again.
This time, Fernando Arce sent the pass across the goal area and Carlos Salcido deflected it to Magallon. Mexico hadn't scored two goals against the Americans since a 2-1 win in a World Cup qualifier at Mexico City on March 27, 2005 _ El Tri's last win in the series.
Mexico generated several more scoring chances, but never got another clear shot on the U.S. goal.
The U.S. and Mexico were meeting for the 54th time. Mexico leads the series 29-11, but the Americans have won nine of the last 13 meetings overall, including a 2-1 win in last year's CONCACAG Gold Cup final.
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