"It was purely a tactical decision, nothing to do with Eddie's performance," said Jones.
"The lad was gutted, but I spoke to him after the match and he understands the situation.
"It's hard for players to go on and then come off again, there's no doubt about that."
But Jones insisted: "Eddie's playing well, running into form and his touches are good.
"All he needs now is a goal to be honest.
"When Ipswich were down to 10 men they played three in midfield and we had to match up to them and keep our wide players high.
"It was either Eddie or Jay Bothroyd coming off and it was purely down to tactics.
"Eddie had done his job and it was up to Stephen McPhail to go on and finish the job off."
Jones started the game with Steve McPhail on the bench after his 2 game suspension. With injuries to Ross McCormack and Peter Whittingham, Jones didn't have a full strength squad but he is happy to know he can still field a starting XI, a bench and have players left over not in the 16. Something that was a struggle several weeks ago.
"I felt that was the right team to pick," said Jones.
"But, if I feel it's right to change it next time, I'll change it.
"We now have depth now and I am able to make selection decisions.
"We don't have Ross McCormack or Peter Whittingham because of injuries, but I was still able to have my captain (Darren Purse), Tony Capaldi and Darcy Blake sitting in the stand.
"To have strength in depth is nice. I can lose any player and I have a replacement available.
"I can't wait to get Ross and Whitts back over the next few weeks."
Jones his hopeful that Michael Chopra will play again before his loan spell is due to end on Dec 31st. City have three more games in December at home to Sheff Weds, away to Redaing and at home to Plymouth.
Jones wants Chopra to stay for the season but with the managerial situation at the Stadium of Light up in the air it's unknown what will happen. First though to get him playing again.
"Chops went to block a clearance and the top of his foot caught the underside of an Ipswich player's boot," said Jones.
"He had ice treatment after the game and it looks more of a soft tissue injury rather than anything serious.
"It cramped up on him a little and I felt it was better to get Eddie Johnson out there than have Michael limping about."
City's next game against Sheff Weds is this coming Saturday, ko 3:00pm.