The Sharks will be sweating on the fitness of NSW representative Siosifa Talakai with the centre limping off in the 79th minute after suffering an ankle injury from a hip-drop tackle by Knights forward Mat Croker.
Several players from both teams were involved in a melee midway through the first half when Saifiti rushed out of the line and smashed Matt Ikuvalu.
Sharks skipper Wade Graham was flabbergasted when referee Chris Sutton cleared Saifiti of any wrongdoing after the bunker checked the vision and awarded a scrum feed to Newcastle.
The Knights scored from the scrum win to make it 6-6 and kept pace with Cronulla to be 12-12 at the break before the finals-bound visitors put the home side away in the second half.
Cronulla regained second spot from North Queensland to finish in the top two for the first time since 1999 when they last won the minor premiership.
The Sharks will host the qualifying final, likely to be at PointsBet Stadium, although the NRL is yet to announce the official draw for week one of the playoffs.
Cronulla second-rower Briton Nikora opened the scoring with a soft try before Tex Hoy squared the ledger after the controversial Saifiti decision.
Bench utility Luke Metcalf sprinted the length of the field for the Sharks to regain the lead before Dominic Young did likewise off an intercept before half-time.
After a rev-up in the sheds, Cronulla regained the ball from the restart and Nikora plunged over a few plays later for his second.
When winger Ronaldo Mulitalo sped away for his 16th try of the season and a 24-12 lead it looked like the struggling Knights were going to lay down their arms but they reduced the gap to eight when Young finished off a right-side raid.
(Photo by Mark Metcalfe/Getty Images)
Just when they looked like bridging the gap further, Jesse Ramien sprinted off his goal line to snuff out a Knights chance and run 99 metres the other way for a 28-16 buffer.
Nikora crashed through some tired Knights defence to make it 34-16 before the Sharks ran out the clock in the final stages with star halfback Nicho Hynes given an early shower to ensure he’d be right to face the Cowboys.
Rookie fullback Lachie Miller started the victory celebrations in the final minute of the match when he sprinted through out wide.
The loss meant Newcastle finished the season with a 6-18 record, slumping to 14th after Gold Coast leapfrogged them with their win over the Warriors in Auckland on Saturday.