The striker was unavailable for Saturday's 2-1 loss after his country threatened to invoke a Fifa ruling that would see him suspended following his absence from international duty
A late Demba Ba header was not enough to salvage a point after goals from Michu and Jonathan de Guzman earned a 2-1 win for Michael Laudrup's side, with a number of first-team stalwarts, including Fabricio Coloccini and Yohan Cabaye, missing for the hosts.
Striker Papiss Cisse was also absent from the squad after the Senegal Football Association threatened to invoke a Fifa ruling that would see the player suspended if he featured in the game.
The governing body failed to receive the appropriate medical records from Newcastle following his absence from international duty due to injury and Pardew admitted the uncertainty over Cisse's availability affected his preparation for the game.
"We kept being promised that the decision would be overturned and that Senegal were going to let Papiss play," Pardew told reporters in his post-match press conference.
"We kept waiting and waiting and it was about 1.40pm when we finally found out that wouldn't happen.
"So it did affect our preparation and him missing today was a blow to us. We didn't do anything wrong and he should have played."
The 51-year-old stated a lack of experience cost his side, who now drop into the bottom half of the Premier League table, but refused to criticise his players, instead putting the poor performance down to the club's mounting injury list.
"Until they scored I though we did a pretty good job. The work rate of the team was fantastic, but we were obviously missing a lot of senior players today," he added.
"Probably the most disappointing thing was our reaction to when they scored, we chased the game and conceded a second.
"Its in the last third where we lack a little bit of potency and that was a bit disappointing, but I'm not going to fault the players in their application - they tried their very best against a good side in Swansea, who had a lot more experience on the pitch and that showed.
"Jonas [Gutierrez] was close [to fitness], we were deciding on whether to play him yesterday but we felt it was too risky, we had Papiss taken away from us while Shola [Ameobi] only returned [from international duty] yesterday."
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Pardew explained: "Our next agenda is Europe, and its another home game and that could give us a lift if we win it. It will probably secure qualification and that would at least be one hurdle cleared."
Swansea boss Laudrup was quick to hail the win as his side's "best away performance of the season" and believes his team should have won by more than their one-goal margin.
Laudrup said: "I think it was the best away performance this season, including QPR and Liverpool.
"To come here and play Newcastle, when Newcastle really needed a win after a home loss to West Ham, we knew it would be very difficult for us and still we gave a great performance.
"Without my Swansea glasses, I think I can say we created eight or nine chances which is a big thing to do as an away team. We should have won with a couple more goals, but it was a fantastic win."
The Dane also hailed Spanish forward Michu, who continued his impressive start to life in the Premier League with a well-taken header to open the scoring.
"What you saw today is what he is good at," Laudrup said. "He is a big lad, and when he plays in midfield and we have the ball he can play the possession game, and then when we come forward he arrives well.
"He is not a centre-forward like [Demba] Ba or others, but when he arrives he is difficult to mark, nearly impossible. Its a difficult position to play, but we're delighted with what he's giving us."