Amad, 22, scored a brace in the European fixture at Old Trafford, with the attacker heading his side into the lead in the 50th minute of the contest before netting his second in the 77th minute to secure all three points.
The Ivory Coast international had to be replaced in the 81st minute, though, and Van Nistelrooy has admitted that the forward is now a slight doubt for Sunday's Premier League clash with Leicester City.
"He had to come off, unfortunately. He's being assessed now and I hope he will be available for Sunday but we have to wait and see," Van Nistelrooy told reporters during his post-match press conference.
Amad has had a frustrating few weeks out of the Man United XI, but he put in a man-of-the-match performance against PAOK, and Van Nistelrooy paid tribute to the Ivorian for his performance in Manchester.
Amad scored a brace in Man United's Europa League win over PAOK
"The second goal had everything in it that is Diallo," said Van Nistelrooy. "He fought to win the ball off the defender, then pushed through to take the shot and had the quality to bend it around the goalkeeper.
"He is a great character and a hard worker. He shows that attitude in every training session. Every day in he comes to me and wants to do extra finishing, crossing, one v ones. He is asking how can I improve his shot, and his heading. He is constantly focused on learning and getting better. He is motivated to get the most from his career.
"His qualities are clear, the way he presented himself today was excellent and important for this team."
Amad has not started in the Premier League since September 21, and it remains to be seen whether he will have the chance to be named in the starting side for Sunday's clash with Leicester at Old Trafford.
Man United secured first European win of season against PAOK
Thursday's result moved Man United onto six points from their four Europa League matches this season, which has seen them rise into 15th spot in the table.
"First half wasn't good, that's clear, a very good point. I think we created hardly anything and PAOK neither, they didn't create a lot, so in that sense, we were okay. But we didn't get going," said Van Nistelrooy.
"I think our possession wasn't good enough, we made many tactical mistakes, our shape wasn't good, it was, at times, not low enough and, every time, in that shape that we wanted to play.
"Second half, we were a lot better, we persisted in finding Casemiro and [Manuel] Ugarte in front of the defence, or Amad and Bruno [Fernandes] in the no.10 positions and that's why we started playing better and creating more chances and getting the better of the game, playing in their half more. And as you said, Amad made the difference there with two good goals."
Van Nistelrooy is now preparing his side for Sunday's game against Leicester before stepping aside for Ruben Amorim, with the Portuguese set to officially take charge of the Red Devils on Monday.