The Toon were stunned early before fighting back through goals from Lewis Miley, Anthony Gordon and William Osula.
Howe later said: "It's a moment you never like (going behind). You prepare for a lot of eventualities in your mind before the game and respect every opponent. It can happen. It did happen.
"It was important we responded. The longer it goes on the more anxiety can creep in. What a brilliant finish from Lewis Miley. From that moment we settled into the game.
"Lewis played very well. He brings loads of composure and quality on the ball."
On his half-time subs, he said: "Anthony (Gordon) was forced. Harvey (Barnes) felt something in his quad. The plan was always to play Joe (Joelinton) and Bruno (Guimaraes) for 45 each."
On Osula's goal, Howe added: "He's been waiting for that moment. He's been training hard. He has huge potential and quality. I haven't seen him score many like that. I'm delighted for him.
"I'm very level. We're delighted with the run of form we're in."