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His first was a low shot under the keeper after a strong run into the box; his second a superb curling strike from 25 yards.
Per Frandsen went on to cap victory with a third goal, keeping Latics at the summit after three wins and a draw from their opening four games.
The Latics manager said: "Nathan has the ability in his locker to get a goal out of nothing.
"He has you crawling up the wall at times but all of a sudden he does outrageous things and things you just don't see too often in the Football League.
"I was pleased to see the first one go in and the second was a fabulous goal.
"Brighton came to frustrate us which I understand, with them sitting very deep and not allowing space in behind them.
"Mark McGhee was at our game at West Ham last week, will have seen what our front two are capable of, and was trying to guard against that.
"To a certain extent it worked but then the Duke scored a goal out of nothing just before half-time.
"It wasn't even a chance really, there a good little ball to him by Jason Roberts, and we went in a half-time with our chins up rather than on the floor."
Ellington now has four goals to his name already this term following last week's double at West Ham.
Jewell admitted he hadn't been happy with Latics' play up until Ellington's 45th-minute opener.
He said: "We were average in the first half, there was no atmosphere and no urgency to our play," said Jewell.
"Fortunately we scored at a fantastic time which gave us a lift and deflated Brighton.
"The fact I was disappointed with the first half perhaps shows the sign of a good team in that we didn't play well but won.
"At times we had to come deep to get the ball because Brighton sat back, and we got a little bit impatient.
"Being patient doesn't mean playing at a slower tempo, it just means putting in an extra pass to make something happen.
"It was nice to see Per Frandsen get off the mark with a goal near the end."
Jewell handed Emerson Thome his Latics debut on Saturday, giving him a late run out as a substitute in place of Ian Breckin.
He is likely to play from the start in tomorrow's first round Carling Cup clash at Grimsby, as are a number of players yet to sample first team action this season.
Jewell said: "I put Emerson on because I wanted to give him a few minutes to get a feel of it.
"He is getting fitter all the time and is now pushing for a first team place."
Magno Silva Vieira was on target for Carlisle United in their 3-0 win at Forest Green on Saturday.
The young striker has moved to Brunton Park on a month's loan in order to get first team experience.
Mike Flynn also made his debut for Blackpool after joining the Seasiders on a similar loan deal.
He helped Colin Hendry's League One side pick up their first point of the season from a 1-1 draw at Hartlepool.