The Magpies will head for Eastern Europe next Thursday night firmly believing they should be doing so with a two-goal advantage after Cisse was denied by the offside flag either side of half-time in Thursday night's 0-0 first leg draw at St James' Park.
That might have flattered Alan Pardew's side slightly after Metalist showed few signs of ring-rust following their mid-season break.
However, Cisse insisted he and his team-mates will swallow their disappointment and do everything they can to ensure those contentious decisions do not prove too costly.
The 27-year-old said: "I think they were both goals, but it is down to the linesman. He said 'no' and once he's made his decision, it's a no.
"There's nothing you can do.
"It's so frustrating. We should be talking about a win. That would have been very, very good for the team.
"The other team tried very hard and denied us. We just couldn't get the win.
"But we can win the second leg and we will be going over there to give it everything. We are confident of still doing the job and getting through."
Cisse's disappointment was compounded by his failure to convert any of a series of other chances which came his way, including a close-range stoppage-time header.
However, at least one and possibly both of the attempts with which he did find the back of the net should not have been disallowed by Norwegian referee Tom Harald Hagen on the advice of assistants Dag-Roger Nebben and Magnus Lundberg.
Moussa Sissoko was belatedly adjudged to have been in an offside position as he set up Cisse with 23 minutes gone with replays confirming he was not, while the striker himself was penalised for going too early before turning home Mapou Yanga-Mbiwa's 74th-minute cross with the decision much tighter on this occasion.
Defender Steven Taylor said: "After the game, the players thought we should have had the two goals.
"Speaking to Moussa, he said he was onside. He was sprinting that way and the left-back was sprinting out. You have just got to get on with it and live with it.
"I thought the performance was spot on. We caused them so many problems. They caused us one or two problems in the first half, but at this level, you are going to get that."
But if Pardew and his players left St James' Park bristling with a sense of injustice, they did so also knowing that they remain very much in the tie, although facing a battle to secure a place in the last 16.
They will run out at the Metalist Stadium in sub-zero temperatures to face a side which did more than enough on Tyneside to demonstrate that they will be a handful on their own pitch, but knowing a score draw would be enough to see them through.
However, 27-year-old Taylor, Steve Harper and Shola Ameobi in particular will need no reminding of the last time they faced such a task in the forerunner of the competition, the UEFA Cup, in May 2004.
The Magpies travelled to Marseille in the second leg of the semi-final having drawn 0-0 at St James' in the first, and returned with their dreams in tatters after losing 2-0 to a Didier Drogba double.
Taylor, who had made his European debut in a 3-0 away victory over Real Mallorca earlier in that campaign, knows exactly what is at stake in Ukraine, and has no doubts the Magpies can get the result they crave.
He said: "They have got to be worried about our players. Ability-wise, we have the better players.
"We have got a lot of international players who have played on the big stage. They know what to expect.
"If we play like we did [on Thursday night], we will be all right."