Horschel finished with a steady round of 69 to leave him 14 under for the week, two shots clear of Bubba Watson who recorded a third consecutive round of 66.
The American is now second in the FedEx Cup rankings going into next week’s Tour Championship with Chris Kirk, winner of the Deutsche Bank Championship last week, leading the way.
Horschel was in a good position to win that tournament last week, but ended up in a share of second and was glad to get a modicum of redemption.
“It just means a lot,” he said. “I haven’t had the greatest season and I had my game today.
“I couldn’t have had a better warm-up session this morning and I played the first couple of holes good and then I was just grinding it and I made some big putts.
“This feels good. Obviously after last week a lot of people on Twitter and out there wanted to call me a choker. I didn’t choke, I just hit a bad swing at the wrong time. I was coming from behind, you don’t choke coming from behind. To lead this thing, to have the three-shot lead, to hold on, means a lot.”
The 27-year-old is now hoping he can take some momentum into next week as he aims for the $10 million (€7.7m) bonus that comes with wining the FedEx Cup.
“My form is really good, I’m putting good, I’m doing a lot of good things well,” he added. “I’ve got my teacher Todd Anderson coming into town and I’m just going to clean up a couple of things.
“I’m a momentum player and if I can just keep what I’ve been doing this week and the last two weeks, who knows what’s going to happen?”
Horschel had three birdies and two bogeys on the front nine, but came home in nine pars to hold off Watson, who had six birdies and two bogeys.
Morgan Hoffmann was a shot further back after following up Saturday’s 62 with a 63 to fire himself into the top 30 of the FedEx Cup rankings and earn himself a place in Atlanta next week.
Ryan Palmer was the only other player who started the week outside of that group to muscle his way in and he finished with a 71 to sit two shots behind Hoffman alongside Jim Furyk, Sergio Garcia and Rickie Fowler.
“I’m really excited,” he said. “More excited about being in all the Majors next year. It’s been a dream of mine to be in the Masters so I’m really pumped.”
Coming into the closing stages, it looked as if Garcia was going to be Horschel’s closest challenger after reaching the turn in 29 and picking up a further shot to stand on the 17th tee just two shots behind.
But the Spaniard put his fourth shot from behind the green into the water and could not get up and down from the resulting drop to leave him with a triple-bogey eight.
World No 1 Rory McIlroy, who heads to Atlanta fourth in the rankings, was a further shot back alongside Adam Scott and Jordan Spieth after shooting a 66.
Keegan Bradley withdrew from the tournament on Saturday and saw himself drop out of the top 30, while defending champion Henrik Stenson did not do enough to get himself through to next week.
1 Rory McIlroy (Ireland) 11.36
2 Adam Scott (Australia) 9.23
3 Sergio Garcia (Spain) 7.87
4 Henrik Stenson (Sweden) 7.81
5 Justin Rose (England) 7.27
6 Bubba Watson (USA) 7.23
7 Jim Furyk (USA) 7.22
8 Jason Day (Australia) 6.79
9 Matt Kuchar (USA) 6.60
10 Phil Mickelson (USA) 5.87
11 Rickie Fowler (USA) 5.81
12 Martin Kaymer (Germany) 5.36
13 Jordan Spieth (USA) 5.22
14 Tiger Woods (USA) 5.13
15 Zach Johnson (USA) 4.87
16 Dustin Johnson (USA) 4.80
17 Graeme McDowell (Irl) 4.77
18 Jimmy Walker (USA) 4.37
19 Hideki Matsuyama (Japan) 4.35
20 Hunter Mahan (USA) 4.16
21 Charl Schwartzel (Rsa) 4.10
22 Victor Dubuisson (France) 4.07
23 Billy Horschel (USA) 4.06
24 Chris Kirk (USA) 3.92
25 Steve Stricker (USA) 3.86
26 Keegan Bradley (USA) 3.84
27 Jamie Donaldson (Wales) 3.79
28 Patrick Reed (USA) 3.73
29 Thomas Bjorn (Denmark) 3.68
30 Jason Dufner (USA) 3.57.
62 Shane Lowry (Ireland) 2.19.