He becomes Mexico's fourth coach in their qualifying campaign for Brazil 2014, and has a two-leg play-off against New Zealand to negotiate next month, from which the winning team will advance to the tournament.
Herrera, coach of Liga MX side America, who lead the Apertura, follows Vucetich, Jose Manuel de la Torre and Luis Fernando Tena in holding the post.
His appointment was confirmed at a press conference where Mexican federation president Justino Compean said: "It's not the ideal situation, nobody likes to be changing coaches. When results are as they are, you have to make decisions.
"We are confident that Miguel Herrera will secure qualification."
Vucetich only led the team for two games.
Appointed on September 13, the 58-year-old former Monterrey boss oversaw a 2-1 win over Panama and a 2-1 loss to Costa Rica, as Mexico finished fourth in the CONCACAF qualifying zone.
Mexico would have missed out on the play-off had Panama not shipped two late goals to lose 3-2 to the United States in their final game.
Vucetich, who is nicknamed King Midas, said in newspaper La Cronica de Hoy: "It was an experience. It was positive, but not what I wanted. It ends like this.
"I'm cocky, I'm King Midas, not God."
Mexico play New Zealand on November 13 and 20.