Robbie Keane opened the scoring on the stroke of half-time of the first leg of the Western Conference final, heading in Landon Donovan's cross.
Magee then got the second on the break in the 64th minute before finishing from close range three minutes later.
The Houston Dynamo scored three times in the second half to come from behind and establish a 3-1 advantage in the Eastern Conference final against DC United.
United were ahead after 27 minutes through Nick DeLeon's shot which deflected in off Andre Hainault, who then levelled the game up in the 51st minute.
Will Bruin completed the turnaround in the 68th minute with an effort that went in off the post before Kofi Sarkodie added a third nine minutes from the end following a one-two with Luiz Camargo.