Gary O'Neill fired Shamrock Rovers to within touching distance of Europe’s group stages with a 96th minute wonder goal.
But Stephen Bradley was frustrated that the Hoops let Shkupi back into the tie at a time when the hosts were on top.
Shkupi’s goal with 13 minutes to go threatened to make Tuesday’s second-leg in North Macedonia a nery affair.
And even more so with influential midfielder Chris McCann limping off in the second-half here with a calf injury .
But O’Neill’s stunning goal gives the League of Ireland champions more breathing room as they look to seize their destiny.
Rovers boss Bradley said: “I’m delighted to win and score three goals, but I’m slightly frustrated at parts of the performance.
“We were slightly sloppy and let them back into the game to get a foothold in the second-half.
“We took our foot off when we had them and that was frustrating because we should have gone for them.
“But Shkupi showed us that they were capable of scoring in that second-half and I think we’re in for a right game next week.”
But Bradley appreciates the value of O’Neill’s goal and taking a 3-1 lead into the second-leg rather than a 2-1.
“It could be huge,” he said. “We saw that in the Ludogorets game. What we do know is that we’re in for a right game as I said.
“But we felt we needed to go for it rather than accepting the 2-1. We feel the third goal could be really important.
“We kept working it down the sides late in the game and it’s just a great strike from Gary O’Neill.”
On a great European night for Irish clubs, Bradley continued: “Teams across Europe respect us a lot more.
“I saw the first-half of the Pats game in Bulgaria and they were very good and deserved to win.
“The league is going in the right direction and hopefully we can both carry it on in Europe this season.”
Bradley feels McCann will struggle to feature in Tuesday’s game in Skopje with such a tight turnaround.
“It’s a calf. He was excellent and was controlling the tempo as they pressed us quite aggressively as we knew they would.
“We lost our way for about 15 minutes when he went off.”
But Bradley revealed that Jack Byrne is in line to make his return from injury in North Macedonia.
“I think Jack will be ready on Tuesday. He worked really well before the game tonight.”
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