Bruno and Joelinton were both part of the Brazil squad that played friendlies against South Korea and Japan and as a result didn't get back to Newcastle's training base until late in the week.
But both were named in the starting XI at the Amex Stadium as Howe opted to name the same side for the third successive game.
Newcastle went into the international break on a high after wins over Union Saint-Gilloise and Nottingham Forest, but slumped to a 2-1 defeat at Brighton after Danny Welbeck's double.
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Explaining and defending his selection, Howe said: "If you're talking about Joelinton and Bruno, they would be the two.
"Lewie Miley hadn't trained for two weeks and Jacob Ramsey is just back from a long lay-off himself, so they're difficult players to bring in themselves because they haven't been 100% match fit either.
"So we made the decision to go with the two lads that have done the travelling."
Joelinton struggled in the first half and was replaced by Miley, while Ramsey returned to action for the first time since late August later in the second period.
Howe added: "Bruno had a much better second half than he did the first, so maybe that's not pure fatigue."
Newcastle could have no complaints at being behind at the break after a poor first half, with Welbeck scoring the opener four minutes before the interval.
Jacob Murphy was introduced alongside Miley at the break and the Magpies improved. Nick Woltemade levelled for the visitors with a sublime backheel on 76 minutes and United looked the more likely winners, only for Welbeck to fire his second six minutes from time.
Howe confirmed his half-time changes were "tactical", saying: "I wasn't happy with the first half and I think it was a time to try and shake the team up, to try and get new energy onto the pitch.
"Different players with different qualities, and I thought the team benefited.
"I thought we'd actually made a bright start to the game and looked in a good place initially, but then we fell away from that and we were loose with the ball in that first period and ended up being in transition an awful lot.
"We didn't play with our normal clarity on the ball. Much better in the second half, much more like ourselves and in the end we're really disappointed to lose.
"We were much better with the changes in the second half, I thought it was a much brighter performance and much more like ourselves."
On Welbeck's winner, Howe said: "It's a big moment. We're chasing the winner. We feel we're the better team in that moment in the game and we're chasing the goal. We want to win games.
"Our midfield line gets penetrated and the ball ricochets to Welbeck.
"He finishes it very well but we're disappointed with the two goals conceded."