Bayern Munich midfielder Shaqiri sent the Swiss in front with a cracking goal from just outside the area in the sixth minute.
FINAL GROUP E STANDINGS
France Played 3, Won 2, Drawn 1, Goals for 8, Goals against 2, Points 7
Switzerland Played 3, Won 2, Lost 1, GF 7, GA 6, Points 6
Ecuador Played 3, Won 1, Lost 2, GF 3, GA 3, Points 3
Honduras Played 3, Lost 3, GF 1, GA 8, Points 0
The No.23 showed some great individual skill to beat a defender and then blast the ball past a helpless Honduras goalkeeper Noel Valladares into the top corner.
Play slowed down a bit after Shaqiri's stunning strike, though Honduras did try to build up possession in the midfield.
But Shaqiri had other ideas as he scored again in the 31st minute to double Switzerland's lead.
Swiss striker Drmic Victor capitalised on a Victor Bernarndez's mistake in the midfield to pass it onto Shaqiri, who calmly tucked it in the lower corner.
Shaqiri became the hattrick man in the 71st minute when he netted an assist from Drmic again to seal his team's pre-quarterfinal entry.
Switzerland will face Argentina in the pre-quarterfinal at Sao Paulo on July 1
Meanwhile France coach Didier Deschamps would not have been too pleased with the draw against Ecuador but the side did dominate proceedings at the Maracana.
France, who had scored eight goals in their two previous games, powered forward from the start.
But through luck, determination, bad finishing and brilliant goalkeeping by Alexander Dominguez.
Ecuador were left with 10 men after skipper Antonio Valencia was red carded in the 50th minute when he lost a challenge against Lucas Digne and the Manchester United player was dismissed by the referee.
For France, Karim Benzema and company kept their fans on tenterhooks as the forward line missed many a chance when the 'Brazuca' kept finding the pole, goalkeeper and the advertising hoardings instead of the net.
Ecuador also had a few good run ins but not enough to threaten the group leaders France.
Switzerland though will have a tough outing against tournament favourites Argentina in the pre-quarterfinals while France will take on Nigeria in the last 16.