Just as the Magpies' injury crisis looked to be easing, both Schar and Joelinton were forced off in the first half of Saturday's match, with the former replaced by Emil Krafth in the 14th minute and the latter swapped for Lewis Miley on the 36-minute mark.
Seventeen-year-old Miley went on to score his first senior goal for Newcastle to break the deadlock just before the hour mark - becoming the Magpies' youngest Premier League goalscorer - before strikes from Miguel Almiron and Dan Burn sealed a much-needed victory for the hosts to end a three-game losing streak.
Howe has since confirmed that both Schar and Joelinton have sustained muscles injuries which could rule them out of next Tuesday's EFL Cup quarter-final clash with Chelsea, but the Newcastle boss hopes that they will not be on the sidelines for too long.
"Obviously, the injuries are the negative," Howe said as quoted by the Northern Echo. "I think Fabian's is a glute problem - I don't think it's a hamstring - but Joey's possibly might be a hamstring.
"We don't think they're serious, but certainly to come off the pitch, they're short-term problems for us that we can't navigate easily at the moment.
"We were thinking that possibly we were through the worst of our injury situation. Now it's reared its head again in a negative way, so we'll have to see where we are."
Both Schar and Joelinton are set to join Harvey Barnes (foot), Jacob Murphy (shoulder), Elliot Anderson (back), Matt Targett (hamstring) and Javi Manquillo (groin) in the treatment room.
Meanwhile, Alexander Isak was left out of the matchday squad for the win over Fulham, with Howe revealing that he opted to rest the striker who has only recently recovered from a groin problem.
"Alex isn't doing too bad," said Howe. "He's been playing recently, but still isn't 100% with a groin problem. We just felt today was probably the right time to take him out.
"He's put himself on the pitch for us because Callum [Wilson has] not been fit, and he's played a lot of minutes. But he's not 100% fit, and I want to try to get him 100% if physically possible. But with the further injuries we've had, I don't know if that will be the case."
On a positive note, Sven Botman returned to the matchday squad for the first time since September after recovering from a knee injury, and the defender came on as an 83rd-minute substitute.
"[Botman is] a very, very popular member of the dressing room, popular in terms of personality, but also as a player," Howe added. "The lads love him on the pitch.
"He's had a really difficult injury, it's not been clear-cut for him. We're really hopeful he can stay fit now, He's back, he's a key part of our plans."
Burn, Longstaff and Callum Wilson all started against Fulham having recently recovered from injury, while Kieran Trippier will be able to return to the side next week after serving a one-match suspension this weekend.
Newcastle's win over Fulham has seen them climb to sixth in the Premier League table and move to within five points of fourth-placed Manchester City, who drew 2-2 at home to Crystal Palace.