Gordon, Newcastle United's top scorer and the subject of formal transfer approaches from the German champions, had missed victories over Arsenal and Bournemouth in April with a hip flexor problem. He returned to fitness in time for the Brighton and Nottingham Forest fixtures but was unused from the bench on both occasions.
Howe explained the reasoning to BBC Radio Newcastle after Sunday's 1-1 draw at the City Ground, where former Newcastle midfielder Elliot Anderson equalised Harvey Barnes's opener for Forest.
"It was tactical. The team has performed well in Anthony's absence. We have gone with more solidity — with Joelinton playing wide and one winger on the other side — to try and strengthen us defensively, because we weren't happy with how we were defending. Since January, really, we have been disappointed. So a change of structure. Ant has come back to fitness, he's training well — but I'm also looking at the future."
He expanded on that forward-looking approach, framing the final weeks as an audition for next season.
"We've got one eye on the future. That's been clear with some of the decisions that I've made with the team — because we want to see some players and see how they are going to grow into the team. It's our duty to try and look to the future and see what the new team is going to look like next year."
Howe praised the contributions of midfielder Jacob Ramsey and Barnes when they came on as substitutes.
"I thought Jacob Ramsey was magnificent when he came on. He really made a big difference. As did Harvey. So it was great to see players stepping up and grabbing their opportunities."
The selection of Lewis Hall, a left-back by trade, at right-back — given that Miley, Tino Livramento and Kieran Trippier were all unavailable or being rested ahead of their summer departure — underlined the depth of Newcastle's injury problems at full-back.
Bayern Munich have made a formal approach for Gordon, with Newcastle insisting no bid close to their asking price has arrived. Whether Howe is managing the player's situation with a potential summer sale in mind adds a further layer to his conspicuous absence from the starting lineup.