Honduras finished bottom of the group with three defeats in as many games.
Kosovo-born forward Shaqiri enjoyed a memorable afternoon as he linked up brilliantly with striker Josip Drmic, who replaced Haris Seferovic in the starting line-up.
Having missed an early sitter, Shaqiri unleashed a sixth-minute thunderbolt into the top left corner and then steered the ball past keeper Noel Valladares on the half-hour mark after he was released by Drmic.
Roared on by chants of "Go Suisse" from their fans in the Amazonia arena, where humidity reached 88 percent coupled with a temperature of 26 degrees Celsius, the Swiss proved too hot to handle for their modest rivals.
Valladares twice denied Drmic in the closing stages of the first half, which produced one-way traffic with Honduras failing to muster a meaningful attempt at goal.
The Hondurans, cheered by most neutral fans, were more purposeful early in the second half and nearly pulled one back when Swiss defender Ricardo Rodriguez cleared Jerry Bengtson's shot off the line.
It was a wake-up call for the Swiss and Shaqiri came close to adding a third, forcing another good save from Valladares before Honduras had a penalty claim waved away after Jerry Palacios went down under a challenge from Johan Djourou.
Spurred by Mexican waves on the terraces, Honduras threw men forward and were caught cold in the 71st minute, when Drmic's good work down the left flank presented Shaqiri with a simple tap-in.
