Flanagan won the 18th hole to defeat David Oh, 1-up, in one of Saturday's semifinal matches while Wittenberg hammered Lee Williams, 5 and 4, in the other semifinal.
Flanagan and Oh were even when they reached the 18th hole but Oh made a mess of the hole when his approach went through the green. Oh was left with an impossible chip and left with a double-bogey-6. Flanagan made a routine two-putt par to advance to the final.
With his trip to the final, Flanagan, an Australian who came to the U.S. to golf a few months back, will receive invitations to both The Masters and U.S. Open next year.
'Just to have the invite to the Masters and U.S. Open for next year is great,' said Flanagan. 'I think I will be a lot more relaxed Sunday, win or lose. I could lose, 9 and 8, and be a lot calmer than I was today when I was 3-up.'
Flanagan did build a 3-up lead through seven holes but things went downhill rapidly from there. He dropped the next five holes to fall 2-down but Flanagan won the par-3 13th when his 6-iron stopped two feet from the hole and Oh conceded.
Flanagan also won the 14th to square the match and the duo halved the next three holes with pars. Then Oh botched the last and now Flanagan can become the first Australian to win the U.S. Amateur since Walter Travis won in 1903.
'I guess today I just started thinking about getting to the finals,' said Oh. 'I started thinking about majors and holding that trophy. You can't do that. It's a cardinal sin. You live and learn and hopefully I can learn.'
Wittenberg and Williams traded wins on the first two holes but Wittenberg took command from there. He won two of the next three holes to go 2-up and then won three holes in a row from the ninth to essentially put the match away.
When the pair parred 14, Wittenberg advanced to the final.
'It's just awesome,' said Wittenberg, who will represent the United States in the Walker Cup. 'I'm just fortunate to be in this situation that I'm in.'
The 36-hole final will take place Sunday.
The U.S. Amateur is one of 13 national championships conducted annually by the United States Golf Association, with 10 of the events strictly for amateurs.