Wednesday have come away victorious just twice in their last twenty league game and manager Jos Luhukay said: "Over 90 minutes, we have a team with no belief. They have not the confidence to play offensive and create chances.
"We had maybe only two or three chances and it was not enough to make a result. Ipswich had three chances and scored two times.
"When you have not a result, you must win games to get confidence back. They must stay together.
"We now have three days to speak with each other and Saturday is a new chance to do it better than we did today.
"It is positive that teams below us also lost, but we must look to us and not to other teams. We have to make a good step forwards.
"This team can play better. We win together and we lose together. They must believe in each other and come away from this situation."
The results moves the Tractor Boys into the top half of the Sky Bet Championship table, and McCarthy felt his side were good value for their three points.
"I think overall we deserved to win," he said. "It was a right royal scrap in the first half and we matched them in every department.
"We didn't allow them to play and I thought we just shaded it. In the second, we were the better team.
"It was great to see Waggy get two goals - his second was real quality. He's got a wand of a left foot.
"For him now to get his goals, he can calm down a bit and play his game and he'll get more.
"We had a different threat when Freddie (Sears) came on. He runs in behind and stretches it and he was excellent, as he has been.
"They've all played well and it's been a good team performance.
"I still think it's too much for us to make the play-offs, but I didn't say we'd stop trying."
Waghorn put Ipswich in front early in the second half before Lucas Joao, who had joined the action at the start of the second half, scored an impressive equaliser.
Waghorn's superb free-kick late on sealed victory for Mick McCarthy's men.
Wednesday boss Jos Luhukay made six changes to his starting line-up following Saturday's 4-0 defeat at Bristol City.
It was a very quiet opening with neither side posing a serious attacking threat early on.
Ipswich's Mustapha Carayol and Jonas Knudsen combined on the left wing with the latter sending over a cross to the far post which forced keeper Joe Wildsmith to punch the ball clear.
Carayol was involved again when he laid the ball off to Waghorn, who shot wide.
Wednesday's Jacob Butterfield touched a free-kick to Adam Reach whose effort from distance went well wide.
Ipswich manager Mick McCarthy was forced to make a change in the 25th minute when Carayol went off injured with Freddie Sears taking his place.
Wednesday's Atdhe Nuhiu was denied by keeper Bartosz Bialkowski who made a stunning reflex save to keep out the striker's close-range volley.
When Waghorn threatened at the other end, he failed to make proper contact and Wildsmith gathered the ball comfortably.
Knudsen tried an effort from distance which was deflected wide.
The resulting corner was only half cleared and the ball fell to Cameron Carter-Vickers whose well-struck drive flashed just wide of Wildsmith's left-hand post.
Ipswich were then caught on the break with Butterfield playing the ball through to Nuhiu who saw his shot from inside the area deflected off-target.
Waghorn struck in the 51st minute, firing in from close range after a Sears cross was headed back across the face of goal by Callum Connolly.
Wildsmith made a superb save to prevent the hosts going further behind, turning a header from Sears over the bar.
Wednesday had a penalty appeal turned down after Joao went down in the area following a challenge from Carter-Vickers.
Sears threatened to find a way through when a back-pass was under-hit, but Wildsmith did well to force the striker wide and the chance was gone.
Nuhiu shot wide before Joao (69) equalised with a fine solo effort, producing some neat skill to hold off a couple of defenders as he advanced into the area before slotting the ball past Bialkowski.
Bialkowski then had to be alert to beat Joao to the ball, making an important clearance.
Waghorn scored the winner in the 83rd minute, curling a free-kick from just outside the right-hand side of the area into the far corner of the net.