Jorge Sampaoli's men guaranteed a third-place finish following a 2-1 win over Ecuador, who finished level on points with Uruguay but automatically qualified for Brazil by virtue of a superior goal difference.
Both teams needed just a point in Santiago but the hosts were not prepared to rest on their laurels, with Alexis Sanchez and Gary Medel scoring in quick succession in the first half which ultimately gave them victory.
Sampaoli, who had replaced Claudio Borghi in the middle of the qualifying campaign, told a media conference: "I've met a group of players with hunger for qualification to the World Cup."
"It was very tough in a past moment, but I highlight the effort of this group."
Midfielder Arturo Vidal added: "In the last games Chile showed good, more solid, football and I think we can fight for important things in the World Cup."
Although Felipe Caicedo pulled a goal back for Ecuador, they could not find an equaliser and were left waiting on Uruguay's result with Argentina to determine the final automatic qualification spot.
But Oscar Tabarez's men needed to win by five clear goals at the Estadio Centenario to move into fourth, settling for a 3-2 victory which sets up a two-legged play-off tie against Jordan.
Los Charruas will at least enter that encounter in high spirits following a morale-boosting win over an Argentina side that were missing several key players but were already guaranteed to finish top of the standings.
The hosts twice took the lead through Christian Rodriguez and Luis Suarez's penalty, only to be pulled back on both occasions by former Liverpool forward Maxi Rodriguez, before Edinson Cavani sealed victory just after half-time.
In Asuncion, a brace by veteran defender Mario Yepes gave Colombia a 2-1 win in Paraguay.
Promising winger Jorge Rojas put the Guaranies ahead early in the seventh minute with a right-footed shot that Colombia goalkeeper David Ospina failed to catch.
Colombia's task was then made harder by Freddy Guarin's dismissal just after the half hour, but Jose Pekerman's men valiantly responded in the 37th minute as Yepes headed home before tapping in the rebound in the second half after Paraguay goalkeeper Justo Villar parried a free-kick.
Paraguay end the campaign at the bottom of the standings on 12 points, with Bolivia, who drew 1-1 with Peru, just above on goal difference alone.
Yoshimar Yotun put Peru ahead in the 18th minute, but in first-half injury-time, goalkeeper Diego Penny failed to catch the ball and Diego Bejarano equalised.