The Iron looked on course to claim a point at the Liberty Stadium, but late goals from Scott Sinclair and Stephen Dobbie ensured the Swans continued their 100 per cent home record this season.
In truth United had few complaints about the outcome as the home side were impressive, but Baraclough felt his side had played well and would have deserved a point for their efforts.
"It was a bitter pill to swallow. The lads in the dressing room are distraught," he said.
"Two minutes before Swansea scored their first goal we could have scored. That shows it's a fine line between success and failure.
"The players worked their socks off and I can't fault any of them. We came here and tried not to be defensive. Instead of playing five in midfield like we have done in previous seasons we played two up front and tried to play to our strengths.
"We knew we had to be a tight unit and avoid getting stretched because Swansea have a lot of pace. We came here with a game plan and it so nearly worked for us."
Brendan Rodgers, the Swans boss, conceded his side had to work hard to break down the Iron.
"They [Scunthorpe] were set up well and we had to be patient but I'm delighted we kept knocking on the door. Perseverance is a key attribute in this league," he said.
"We had to change the game around a little bit tactically and instead of finishing 0-0, we have gone on to win the game."