The Magpies' manager admitted the late loss was hard to take but highlighted Wednesday's Champions League clash with Union Saint-Gilloise as a chance for redemption.
Newcastle had looked on course for a statement victory when Nick Woltemade rose highest to head home in the 34th minute, giving the home side a first-half lead against the run of play.
Arsenal dominated possession and created multiple openings, but their frustrations mounted as a penalty decision was overturned by VAR and a powerful effort struck the post.
The Gunners continued to press after the break, only to be denied repeatedly by goalkeeper Nick Pope, who produced a string of vital saves to preserve Newcastle's advantage deep into the second half.
Substitute Mikel Merino eventually found the breakthrough in the 84th minute, powering in a header from a corner to level the contest.
Arsenal then delivered a devastating late blow in stoppage time, as Gabriel Magalhaes met another corner in the 96th minute to complete the turnaround and snatch all three points for Mikel Arteta's side.
Asked about the upcoming Champions League game, Howe said: "The game is a good thing.
"After this painful defeat, it is good that we have another game soon after.
"We want to get confidence."
On the Arsenal defeat, he added: "Two really late goals here at home hurts.
"We have to reflect and acknowledge that we weren't at our best.
"There was not lack of effort but from a footballing side, it wasn't quite there.
"Probably the key thing, the number of corners. I think Odegaard made a difference to their overall performance. The weight of pressure eventually told. No lack of effort but the little details have cost us.
"I thought we tried. We gave everything to the game. It was really physical.
"I don't think we were at our best today being honest - Arsenal played very well."
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