Midfielder N’Diaye opened the scoring at the end of the first half when Simon Mignolet spilled a header from Harry Maguire.
Niasse made sure of the victory with five minutes of the game to go when he latched on to a through ball from Andrea Ranocchia and coolly slotted home to secure all three points.
There were full debuts for Deadline Day signings Kamil Grosiki, N’Diaye and Ranocchia – the latter as a last minute replacement for Michael Dawson who withdrew during the warm-up.
Silva also recalled Omar Elabdellaoui and Abel Hernandez making it five changes from the team which earned a goalless draw at Old Trafford three days ago.
It was a lively start to the game for the Tigers with Hernandez and N’Diaye forcing Mignolet into early routine saves.
Coutinho was causing mayhem on the Liverpool left on the 20th minute mark but Lallana failed to make good contact on his ball in.
The Brazilian then had a chance of his own but dragged his effort wide from within the area.
Maguire picked up the first book of the game for clattering Sadio Mane on the right side of the pitch.
Grosiki was showing good potential on his home debut and almost put in a wicked ball towards Hernandez – Mignolet grabbing the ball just in time.
Liverpool defender Joel Matip saw a header go wide in the 36th minute before Sam Clucas steered a header wide himself at the other end.
The Tigers were to get some reward for a positive first half performance a minute before the interval though when N’Diaye scored on his debut for the club.
Mignolet failed to gather a Maguire header under pressure from Hernandez and the Senegalese international was on hand to knock the ball over the line to give Silva’s men a first half lead.
A succession of corners for the Reds at the start of the second period led to Jakupovic gathering a weak header from Emre Can.
The Swiss stopper had to again be on his toes to tip over a Mane header, Coutinho volleying over the following corner.
Hernandez had an opportunity just after the hour mark after latching onto Huddlestone’s through ball but the striker could only find the side-netting.
The Uruguayan had an even better opportunity a minute later when he raced onto Grosiki’s through ball – Mignolet this time alert to the danger.
The best Liverpool chance of the game fell to Coutinho on 67 minutes but he failed to hit the target from six yards.
With pressure mounting from the Reds, Niasse stepped off the bench and secured all three points for the Tigers five minutes from time.
Ranocchia’s long ball released Niasse who kept his cool under press to put the ball past the advancing Mignolet.
With the clocking clicking down there was still time for Jakupovic to make his customary wonder save.
Henderson’s drive looked set for the back of the net but the goalkeeper did well to deny the England international.
Hull City: Eldin Jakupovic, Omar Elabdellaoui, Andrea Ranocchia, Harry Maguire, Andy Robertson, Tom Huddlestone, Alfred N’Diaye, Kamil Grosiki (David Meyler 80), Evandro (Josh Tymon 62), Sam Clucas, Abel Hernandez (Oumar Niasse 65).
Subs Not Used: David Marshall, Adama Diomande, Shaun Maloney, Dieumerci Mbokani.
Liverpool: Simon Mignolet, Nathaniel Clyne, Lucas Leiva, Joel Matip, James Milner (Alberto Moreno 83), Jordan Henderson, Adam Lallana (Divock Origi 83), Emre Can (Daniel Sturridge 67), Sadio Mane, Philipe Coutinho, Roberto Firmino.
Subs Not Used: Loris Karius, Georginio Wijnaldum, Joe Gomez, Trent Alexander-Arnold.
Referee: Mr L. Mason