Angelo Ogbonna was among those to have been critical of the opposition for their celebrations following last month’s 2-1 victory in Piraeus, a result that ended Moyes’s 17-match unbeaten streak on the continent.
Despite the lingering ill-feeling before the game, however, Thursday night’s clash had largely been a drab affair until Paqueta latched onto a delightful ball from James Ward-Prowse.
The hosts then survived a late scare when Mady Camara hit the post late on to reclaim top spot in Group A after Freiburg had beaten Serbian side Backa Topola earlier in the night.
West Ham are now assured of European football after Christmas and can seal qualification for the knockout stages of this competition by winning in Serbia later this month.
"I'm really pleased that we got the result because the result was the most important thing,” said Moyes to TNT Sports.
"We didn't play as well as we would have liked but they're a decent team and a well seasoned European team and used to coming away in these competitions - more so than we are.
"In the end I think we were the ones who made the best chances, they didn't have too many chances to score. It was a little bit hairy towards the end, but largely we controlled it."