While they remain third in the Welsh Alliance League, victories for Llanrwst and Conwy in their final games could plunder the Lilywhites as low as fifth in the final rankings.
Things began badly for the visitors when Tom Roberts edged the Junction in front, then Adam France conceded a penalty which gave the Railwaymen a chance to double their lead.
Jamie Jones saved Nathan Jones' kick, but the Junction man was first to reach the rebound and he made it 2-0.
Rhyl pulled one back through Mike Roose clear but before the interval Tom Roberts added a third for the hosts.
Rhyl's prolific hitman Marc Lloyd Williams, cup-tied for the first team and unable to feature in the League Cup final, hit the post twice but did pull one back.

THE prolific Steve Bowes rattled in five goals for Prestatyn Town Reserves in a 9-0 massacre at Halkyn United which put the Seasiders on the verge of retaining their Mackenzie Jones Clwyd League Premier Division crown.
Craig Griffiths (2), Chris Evans, Jamie Duffy and John Evans were also on target for the visitors.
Rhyl Nomads' bad run of results continued as they went down 5-2 at Denbigh Town Reserves, goals from Josh Bucknall and Dean Moss their only high points.
The ever consistent Shane Hayes found the net for Rhuddlan Town at Mochdre Sports, but his team ended up 2-1 losers.
Abergele Rovers' title hopes ended with a 4-3 defeat at Penmaenmawr Phoenix despite a hat-trick from Andy Thomas in a match which featured four penalties - two for each side.
In Division One, Betws-yn-Rhos and Abergele Rovers Reserves finished 1-1. Ryan Woods handed Gele a half time lead, but Jordan Lee levelled after the break. Aztec Sports failed to raise a side for their match at Cerrigydrudion.
Prestatyn Town 3rds crashed out of the Halkyn Cup at the semi-final stage, bowing out 2-1 at Aston Park Rangers 3rds.

YOUNG crackshot Jack Higgins fired two goals to help send Rhyl Hearts Milan storming to a 3-0 victory in the showpiece final of the Clwyd Junior League's Under-16s Challenge Cup against Holywell staged at neutral Flint Town's ground.
As well as twin-striker Higgins, Hearts had a powerful performer in Diago Alvirado who netted their other goal and although Holywell tried to close the gap after the break, the Hearts defence was in unyielding form to carry off this prized trophy.
Prestatyn Athletic will be aiming to complete a notable local double when they face Buckley Town in the final of the League's Under-17s Challenge Cup this week, again at neutral Flint.