The Magpies are without Demba Ba, Yohan Cabaye and James Perch for the trip to Belgium, after the trio sustained injuries during Sunday's 1-1 draw at Liverpool.
But, while the 51-year-old expressed frustration at having to juggle a "really stretched" squad, he remains confident of getting a victory which could seal passage to the final 32.
"This is an opportunity to get the qualification sorted, and that's what we want to do," he told reporters.
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"But it's easier said than done because we're all aware of Brugge's qualities after the first game and we're carrying three more big injuries after the trip to Liverpool at the weekend.
"Cabaye, Perch and Demba definitely won't play, so that's three big players that are out of the equation before we've got on the plane. That doesn't give me a lot of options to rest players or shuffle the team around.
"The squad is really being stretched at the moment, and there's no doubt that events at Anfield at the weekend have hurt us."
The Englishman also admitted his side face a tough test against the Belgians, who he believes will try and dominate the game from the first minute.
"It will be a tough game - we're under no illusions about that," he added.
"It's going to be important that we're the ones controlling proceedings from the very first minute. We'll do our best to do that and hopefully that will enable us to come away with another positive result in Europe.
"I'm confident we'll be going there with a strong enough team to hopefully get a win."