The Southeastern Conference's leading scorer had just 11 points as Mississippi clung to a 3-point lead midway through the second half.
He poured in the next 15 points for Ole Miss over a stretch of 3:04 to push the lead to double figures, and the Rebels held on for a 75-64 win on Saturday.
Moody finished with 28 points on 8-of-21 shooting as Ole Miss improved to 7-2.
"Moody, for him, did not have a great statistical night even though he finishes with a ho-hum 28 points, but he made the plays that needed to be made down the stretch," Ole Miss coach Andy Kennedy said.
The Redhawks pulled within 50-48 with 7:21 remaining on Isiah Jones' third 3-pointer of the half before Moody went to work.
Moody knocked down four free throws and a layup before hitting three 3s in a row to push the Ole Miss lead to 63-52 with 3:51 to play.
The Rebels led by as many as 12 down the stretch. Southeast (0-9) cut it to six with 1:56 left, but got no closer.
Ole Miss, which led by as many as 13 in the opening 20 minutes, took a 35-25 advantage into the break.
Ole Miss dominated on the boards, outrebounding the Redhawks 53-36. Marcanvis Hymon had a season-high 14 rebounds, while Sebastian Saiz added 11. The Rebels had 19 offensive boards, scoring 17 second-chance points.
"I think that's the best thing that Ole Miss does and I think that's one of the best things that they've always done because they've always had an elite scorer like a Moody or a Marshall Henderson that you have to pay so much attention to," Southeast Missouri coach Rick Ray said. "Then all of a sudden you're helping, helping, helping and all of a sudden they're on the glass."
Antonius Cleveland scored a career-high 25 points for Southeast Missouri. Jones finished with 15 points and Trey Kellum added 10.
"I thought he did a good job of going in there and knowing when to get to the rim and knowing when to get to his pull up," Ray said of Cleveland. "But I think what it all boiled down to was I thought we had a much better pace of play, which allowed us to be in attack mode much more."
The winless Redhawks and Ray — who'd spent the last three seasons in the SEC as the coach of Mississippi State — made sure that the first SEC team to ever visit the Show Me Center didn't escape with an easy victory.
The Redhawks scored the first six points of the game and held a 10-5 lead 4:24 into the contest before Ole Miss used a 14-7 run to take its first lead at 19-17 with just over eight minutes to go before halftime. The Redhawks were held to just eight points the remainder of the half.
"Knowing preparation for them, I didn't think anything was wrong with their effort — they're athletic," Kennedy said. "(Ray) tries to confuse you a little bit, a lot like what we do typically. They've just not been able to make shots at a very efficient rate. Tonight we allowed them to make shots early and it gave them confidence."
Ole Miss: The Rebels extended their winning streak to four games. ... Ole Miss shot 34.7 percent in the game and was 7 of 29 (24.1 percent) from beyond the arc.
SE Missouri: Southeast shot 41.2 percent from the floor and was 5 of 15 on 3-point attempts.
Ole Miss: The Rebels are at home against Louisiana Tech on Tuesday.
SE Missouri: Southeast is on the road at Northern Kentucky next Saturday.