Ibrahimovic scored for the fifth straight game and took his tally to seven this season during the Galaxy's 2-1 win over Houston Dynamo.
However, the star's penalty had been cancelled out by Alberth Elis' spot-kick before Diego Polenta netted an 88th-minute winner.
The win lifted the Galaxy into second in the Western Conference after six wins from seven games.
Ibrahimovic gave his side the lead just after the half-hour mark with a penalty, but Elis had seemingly earned Houston a point.
But Polenta scored the winner, heading in a Jonathan dos Santos corner for the hosts.
Toronto moved into second in the Eastern Conference after a 4-3 win over Minnesota at BMO Field.
Darwin Quintero's brace — which included a penalty in the 70th minute — had put Minnesota 3-2 up after Alejandro Pozuelo's double for Toronto.
However, substitute Jordan Hamilton, introduced in the 73rd minute, proved to be the match-winner for the hosts.
Hamilton put away a Jonathan Osorio pass to bring Toronto level before scoring the winner in the 79th minute, heading in from close range after Jozy Altidore had lobbed Minnesota goalkeeper Vito Mannone.
The visitors were reduced to nine men late on as Jan Gregus and Francisco Calvo were sent off.
Meanwhile, Albert Rusnak's brace led Real Salt Lake to a 3-0 win over Cincinnati.