After trailing 1-0 at half-time to Eran Zahavi's impressive strike, Honduras hit back just after the break through Roger Espinoza.
But Maynor Figueroa's own goal gave Israel the ascendency soon after, before goals from Omer Damari and Gil Vermouth saw Eli Guttman's men defeat Honduras for the second time in a year.
The victory was Israel's first since they triumphed 2-0 over Honduras on June 2, 2013, and their first win in eight matches.
Honduras generally struggled to open up Guttman's compact 4-5-1 formation at BBVA Compass Stadium, while Israel's sharp passing was too much for the CONCACAF nation's defence in a worrying sign for their Colombian coach Luis Fernando Suarez.
Espinoza and Mario Martinez started on the flanks for Suarez's side, while Donis Escober took the gloves ahead of Noel Valladares.
While Honduras had plenty of possession in the opening 15 minutes, they barely tested Israel's goalkeeper Ariel Harush until Marvin Chavez's powerful drive just after the 20-minute mark.
As the half wore on, Israel gained momentum with Zahavi thumping a shot over the bar in the 25th minute before Escobar had to punch Bibras Natkho's long-range effort away.
Sheran Yeini got his head up in midfield, slipped the ball forward to Zahavi, who took a touch and then unleashed a 20-yard shot past Escobar's outstretched left hand and into the net.
It should have been 2-0 just two minutes later when Escobar came off his line and missed Vermouth's cross but Damari could only glance his header wide of the post.
And while Honduras started brightly, equalising in the 47th minute when Espinoza struck a fine effort over Harush and inside the far post, they were behind again six minutes later when Figueroa deflected Tal Ben Haim's shot past Escobar.
On the hour mark it was 3-1 when Vermouth's shot came off the post and Damari converted the rebound, while the former extended Israel's lead further with 16 minutes remaining, finishing from inside the penalty area.
While Costly's late goal gave the Honduras fans something to cheer about, Suarez and his men have plenty of work to do ahead of the World Cup.
