Aubrey Ngoma and Elias Pelembe during the Telkom Knockout match between Mamelodi Sundowns and University of Pretoria.
AmaTuks made their first appearance in the top-flight cup competition on Tuesday and Barker was pleased with the effort shown by his outfit.
"We had a game plan. We knew that Sundowns were under immense pressure and it was in our game plan that we don't concede early," Barker said.
"We threw caution to the wind in the last 20 minutes. I though we started getting back into the game and maybe we were just a little bit unlucky that one or two things didn't fall for us."
Barker admitted the Brazilians took control early on, but he felt his side had looked in contention going into the half-time break, before an early Elias Pelembe second-half goal put the troubled Sundowns side in front.
"We did sit a bit deep in the first half and allowed them a lot of possession but they weren't really threatening," Barker said.
'Keep it tight'
"We went into half-time thinking that things were going well. It was again a situation of the first 10 or 15 minutes in the second half where we had to keep it tight and then maybe start taking the game to them.
"Unfortunately Elias Pelembe showed a little bit of class. They created an opportunity and they scored the goal."
With the cup now out of reach for the league newcomers, Barker turned his attention to the Premiership, with Tuks set to meet Sundowns at the same venue on November 10.
"We know Sundowns are a quality team, with quality players all round," he said.
"They are good on the ball and I think a big pitch like this [at Loftus] suited them.
'A lot tougher'
"We play them in the league in a couple of weeks' time and I think it will be a lot tougher for them."
Earlier, in first-round matches, AmaZulu recovered from a poor run of form to beat Platinum Stars 2-1 in Clermont on Sunday, and Bloemfontein Celtic staged a gutsy late fight back to defeat Chippa United 2-1 in Cape Town.
On Saturday, Maritzburg United beat Moroka Swallows on penalties after a goalless encounter at Harry Gwala Stadium, and Collins Mbesuma scored a brace as title holders Orlando Pirates defeated Black Leopards 2-0 in Polokwane.
SuperSport United edged Ajax Cape Town on penalties, with the sides level at 1-1 after extra time, and Free State Stars dumped Golden Arrows from the cup competition with a 3-1 victory in Bethlehem.
On Friday evening, Wits had kicked off the last 16 action, pulling off a shock 3-2 win over league leaders Kaizer Chiefs at Bidvest Stadium. – Sapa