The hosts went into Thursday's clash with their arch-rivals needing only a point to secure their first Leaders' Shield for four years in front of their own supporters, but Warrington spoiled the party.
Joel Monaghan ran in two of the Wolves' seven tries as they ruthlessly picked apart Nathan Brown's side to silence the home crowd.
Stefan Ratchford also crossed for the visitors and was successful with four conversions, while Michael Monaghan, Gareth O'Brien, Richie Myler and Ryan Atkins also went over to ensure scores from Shannon McDonnell and Willie Manu were in vain for the home side.
St Helens must now regroup and attempt to seal top spot in the final round of fixtures in the regular season at Brown's former club Huddersfield Giants on Friday, when they will win the Leaders' Shield if they avoid defeat.
Warrington's victory ensured they are in fourth spot, but it came at a cost as loose forward Simon Grix sustained a suspected broken ankle.
Castleford Tigers are the only side that can overhaul the leaders after they withstood a Wakefield Wildcats fightback to win 26-22 at The Jungle on Sunday.
James Clare scored two tries as the Tigers raced into a 22-10 lead at half-time and although two tries in as many minutes from Scott Anderson and Richard Owen gave Wakefield hope, the home side held on.
Castleford travel to Perpignan to face Catalan Dragons next Sunday knowing they can claim the Leaders' Shield if they win and Saints suffer another defeat.
Wigan Warriors took a giant stride towards securing a top-four finish courtesy of a 21-6 victory over Leeds Rhinos on Friday.
Shaun Wane's men led 14-0 at the break and Leeds failed to mount a response, so the Challenge Cup holders are now unable to finish in the top four and the third-placed Warriors only need to avoid defeat at home to Warrington to ensure they will not end up outside the top four.
Wigan, Warrington and Huddersfield Giants are all level on 35 points after the latter saw off Hull FC 38-28 on Sunday.
Josh Griffin helped himself to 30 points as Salford Red Devils heaped more misery on sorry London Broncos by hammering the bottom side 58-26, while relegated Bradford Bulls were beaten 32-12 by Widnes Vikings at Odsal.
Catalan consigned Hull KR to a 32-14 home defeat in the other game to be played on Sunday