Donovan scored either side of half-time for the USA thanks to passes from Bedoya, while the former also set up Eddie Johnson's opener at Cowboys Stadium.
Honduras made it 2-1 seven minutes into the second half on Wednesday when Nery Medina sent a thumping header past USA goalkeeper Nick Rimando but Donovan hit back immediately to clinch victory for the hosts.
But the USA may be without head coach Juergen Klinsmann for Sunday's Gold Cup final after the former German striker was sent to the stands with three minutes remaining against Honduras.
Klinsmann reacted angrily to a hard challenge on American full-back DaMarcus Beasley and referee Walter Quesada banished him from the bench, however CONCACAF have yet to rule on whether the USA's head coach will be suspended from the final.
Johnson gave the USA the lead in the 11th minute in Arlington, Texas, with the Seattle Sounders striker bursting onto Donovan's sharp pass, before finishing from just inside the area.
Donovan made it 2-0 on 26 minutes when he chested down Bedoya's lobbed pass and then slotted the ball past Honduran goalkeeper Donis Escobar.
Honduras gave themselves a chance of a comeback with Medina's powerful header from Marvin Chavez's 52nd-minute corner, but when Donovan tapped in Bedoya's cut-back a minute later, the USA effectively wrapped up the win.
The USA, who have not won the Gold Cup since 2007, will face Panama in the tournament's decider after the Central Americans stunned Mexico 2-1 in the other semi-final at Cowboys Stadium.
Blas Perez opened the scoring for Panama in the 13th minute but the match was level at half-time after a diving header from Mexican midfielder Luis Montes on 25 minutes.
Panama had not reached a Gold Cup final since 2005 when they lost to the USA on penalties, but ended that drought thanks to Roman Torres' crunching header just after the hour mark, before holding on for a famous win.
