Ton looked comfortable in the first half before running out of steam in the second and going down to a barrage of second-half strikes from the home team.
Duffy believes his side were unlucky to lose by such a margin after they proved in both legs of the tie that they could compete with their opposition.
Whilst he admits the Tangerines were deserving of their win, he says his boys’ hard work merited a more apt scoreline.
He said: “It was similar to Tuesday night a little bit, really.
“The first half I thought we were outstanding but the second half I think United took control of the game after they got the first goal and then won the game comprehensively.
“But I think the scoreline is definitely harsh on us, if you look at the amount of effort we put into the two games. I’m not saying we deserved to win because we didn’t, Dundee United were clinical and you need that firepower to see you through.
"But it was still a harsh scoreline for our boys considering the amount of work they put in.
“I thought in the first half tactically and energy levels we were great, we tried to make it difficult for Dundee United and not allow them to get into the game early on.
“We thought they’d come out the traps but we managed to keep them pressed back, but they’ve got real quality in key areas and when those moments of quality are required they came up with the goods.
“We congratulate Dundee United, they’re an outstanding team, a huge club. I wish Ray McKinnon well in the play-offs as I do Peter Houston. It’s two terrific clubs and it’ll be neck and neck between them. I wouldn’t like to call it.”
Duffy is hopeful his team can build on this season’s impressive fourth-place finish going into the next campaign, but he is under no illusions that it will be tough.
With the number of players out of contract in the summer into the double figures, the gaffer knows how difficult it can be to work out.
Having coped with a similar situation last season when Morton lost several key men, Duffy had to rebuild his squad virtually from scratch — making this season’s successes even more impressive. And though he won’t fancy doing so again next year, he believes progress can be made as long as everyone at the club is realistic about the possibility.
He said: “It’s difficult to build at our club because you never know how many players you’re going to have.
"If you’re a top club you can maybe have two or three year contracts and that can help you build over a period of time, even if you might lose one or two. But generally speaking we’re one year contracts with players.
“I’ve got 11 or so players out of contract so it’ll depend on how many of them want to stay, how many can afford to stay.
“What this season has done is raise expectations and that’s not a bad thing as long as we’re realistic about the whole approach. The Championship is a very difficult league, this year with Hibs and Dundee United, we’ve shown that we can cope with that.
“But we need to add at the top end of the pitch. We have fantastic energy, great commitment, but football is about what you do in the opposition penalty box — and that’s something we have to improve on.”