The Magpies looked to be heading for their third successive Premier League defeat and their third on the trot at St James' Park after Charles N'Zogbia returned to haunt them with a quickfire first-half double.
But without ever reaching anywhere near their best form, Hughton's men ground down the Latics and snatched a point at the death when skipper for the day Fabricio Coloccini headed home an equaliser in the fourth minute of added time.
Hughton said: "What we have got in this side is great character, that I am aware of.
"What we are now doing is we are now playing our football in a tougher division, and Wigan have become very much an established Premier League side and they showed very much in patches today the quality they have got.
"We knew we were on the back of two home defeats and that's not something we wanted to continue.
"We know we are in a tougher division, but this is somewhere that became very much a fortress for us last season.
"The only way to get back to anywhere near that, which we know is impossible in this division, is to draw out results in whichever way we have to, and we showed great character and quality towards the end to get back into the game."
Newcastle could not have left it any later to grab their point.
The roar which went up at the stadium when Coloccini headed home his last-gasp equaliser was as much in relief as celebration with the 6-0 demolition of Aston Villa on August 22 now long forgotten.
To make matters worse, it was N'Zogbia who threatened to undo them as he plundered as his 22nd and 23rd-minute strikes put the visitors 2-0 ahead.
The Frenchman gave full-back James Perch a torrid afternoon throughout, and might have eased his side to victory had he made the most of the space afforded him after the break.
But substitute Shola Ameobi gave Newcastle hope with a 72nd-minute header, and Coloccini completed the comeback at the death.
After defeats on Tyneside by Blackpool and Stoke, a point was an improvement, but Hughton, who rested captain Kevin Nolan, acknowledged that his team need to start picking up more results against the sides who are likely to be around them in the table.
He said: "It's always a concern when you are losing or drawing games, and it would be no secret that there are a group of teams against which you would feel that you have got your better opportunities to get your points.
"Over a season, we will have to gain more points from the teams in that group."
For Wigan boss Roberto Martinez, it was a case of what might have been as his side only just failed to hold out.
He said: "The game can be very cruel and that was a clear example.
"I felt we were well in control for the whole game, we scored two very good goals from open play, which is the hardest thing in football, and then we let ourselves down by just not being able to defend a set-play at the end.
"That's a little bit where we are. I feel we are very talented young group of players and we showed that today.
"But then we are lacking that little bit of know-how, that little bit of experience that you need to show at critical moments of the game to see it through.
"Sometimes that can be painful, but the performance as a whole was something we can take a lot from and carry on growing."