The Bermudian international, who last notched in mid-October, scored after 59 minutes against Bristol City - his fourth of the campaign lifted Town up to fourth in the Championship.
Wagner’s side went ahead through Elias Kachunga’s 10th-minute header, his seventh goal of the season.
But Bristol City claimed a controversial leveller by Tammy Abraham after 33 minutes, when Town argued Aaron Wilbaham was offside when setting up the goal.
Head coach Wagner said: “I am very happy for Nahki. His goal came from a mistake by the goalkeeper (Frank Fielding) but Nahki chased him down and deserved that.
“Nahki works very hard and he had a role in the first goal when he made a run to open up the space for Elias.”
Wagner felt Fielding should have been sent off early in the second half - the former Derby County man handled outside his area and Town claimed Wells was denied a scoring opportunity.
Referee Keith Stroud, who also denied Wagner’s side two penalty appeals, showed only a yellow card.
The boss explained: “I thought it was a clear red card.
“While I don’t really like to speak about referees after a match, what I will say is that over recent games, I don’t think we have got the advantage of 50:50 decisions.
“We have to accept this. The referee does his job as well as he can, and sometimes his view may look a little bit different from my view.”
Wagner added: “The players performed very well against a very hard opponent and we are very happy and proud.
“This was a massively huge win for us.
“Twenty games have gone and we have 10 wins, which is fantastic but we can only celebrate for a few minutes before we focus on the next game.”
Meanwhile, Tuesday’s hosts Burton Albion dropped to 20th after a 2-1 defeat at Brentford.