The Americans will take on Panama in Chicago for the tournament championship Sunday after Panama stunned Mexico 2-1 in the second game of the semifinal doubleheader held on the home field of the Dallas Cowboys.
Donovan has scored five times during the CONCACAF regional championship, helping the United States run its current all-time best winning streak to 10 matches.
Donovan found Eddie Johnson on a run down the middle of the field in the 11th minute and Johnson easily beat goalkeeper Donis Escobar.
The United States took a 2-0 lead at halftime thanks to Donovan's goal in the 27th minute.
Nery Media scored on a header off a corner kick in the 52nd minute to bring Honduras within one, but Donovan scored again only a minute later.
United States Coach Jurgen Klinsman was sent off in the second half for arguing the lack of a call on what appeared to be a flagrant foul against an American player.
Tournament rules give CONCACAF's disciplinary committee jurisdiction in determining whether Klinsman will have to miss Sunday's championship game.
Roman Torres scored the winning goal for Panama in the 61st minute, preventing a U.S.-Mexico final for what would have been the first straight Gold Cup event.
Panama scored first on a goal from Blas Perez in the 13th minute, but Mexico tied it midway through the opening half on a score by Luis Mones.
Panama also defeated Mexico 2-1 in the group phase of the tournament.