Williams lost a set for the first time in the tournament and committed 41 unforced errors, 20 more than Wozniacki. Williams will face ninth-seeded Ana Ivanovic in the final. Ivanovic beat fifth-seeded Maria Sharapova 6-2, 5-7, 7-5 in a night match.
Williams beat the 12th-seeded Wozniacki for the eighth time in nine career matches, overcoming a tight lower back.
''It was definitely feeling super tight in the match,'' she said. ''That's when I really relaxed, to be honest. By then I was able just to go for more shots and come to the net more and just kind of just not have anything to lose.''
She also tried to shorten points with booming serves, leading to getting just 58 percent of her serves in play.
''I just had to go for rockets because I wasn't feeling great,'' she said. ''I thought, `Listen, I'm going to go out and just try to hit aces and see what happens.' It started working for me. I was like, `OK.' Hopefully my arm will be OK tomorrow. We'll see.''
Williams and Wozniacki both struggled with their serves, leading to a combined 15 service breaks, including the first five games of the third set. Wozniacki was broken in eight of nine service games in one stretch and connected on just 54 percent of her first serves.
''I didn't get many first serves in,'' Wozniacki said. ''When I did, they weren't placed very well. It's frustrating, because you lose a set 6-4 in the third and you only hold serve once.
''I actually broke Serena three times in the set. I don't think that happens very often to her either, so, you know, you feel like you're there and my all game was there. I was fighting. I was running. I was trying to take the ball early. I was returning well. Then my serve comes around and I can't seem to hold serve. It's frustrating thing when you're out there on the court.''
Williams has never won the Cincinnati-area tournament in five previous appearances. She lost a third-set tiebreaker to Victoria Azarenka last year.
With the win, Williams also wrapped up the U.S. Open Series women's title. Williams has won it three of the past four years and will attempt to set another record for the largest payout in tennis history at the U.S. Open - $4 million ($3 million for winning the U.S. Open and a $1 million bonus for winning the U.S. Open as the series champion).
The two-time defending U.S. Open champion won both the U.S. Open Series title and the U.S. Open last year. She is the only woman to win the U.S. Open Series bonus challenge three times (2011, 2013, 2014). No other woman has won it more than once.
Despite winning his first two service games at love and jumping out to a 4-1 lead, Federer wasn't trying to shorten the match because of its late start - after Ivanovic and Sharapova went 2 hours, 45 minutes.
''I play the same speed at all times,'' Federer said. ''If you start hurrying, then you might get broken. I'm happy with the win. I know Milos can cause difficulties with his game. It's unpredictable. He plays on his terms.''
Ferrer suspected Benneteau, who upset third-seeded Stan Wawrinka in the quarterfinals, might've been nervous about playing in his first ATP Masters 1000 semifinal.
''He (had) a very good week - a very great week - but today, maybe he (made) a little bit mistakes,'' said the Spaniard, who was playing in his 15th Masters semifinal. ''(This) was his first semifinal in one Master 1000. Maybe experience was the key in those moments, no?''
Ivanovic had to fight off nausea that prompted a visit from the trainer in the second game of the third set. That left her even more proud of her second straight win over Sharapova and fourth in 12 meetings.
''It's a very thrilling, I think, moment because it was very competitive towards the end, especially in the third set,'' Ivanovic said. ''Even in the second, lots of turn around, lots of breaks in the third set. Just so, so thrilled and happy to stay composed and fight until the last moment. When it mattered the most, I played some really good tennis.''