Cowdenbeath face a relegation play-off after a stoppage-time equaliser secured a draw for Queen of the South.
McHugh slotted home a dramatic leveller five minutes into time added on to deny the hosts.
Cowdenbeath's Kane Hemmings had missed the best chance of the first half when he headed wide from close range.
But he made amends and gave the hosts hope of finishing above Alloa Athletic when he tucked the ball past Alex Clark with 14 minutes remaining.
However, McHugh's cool right-footed finish from a corner earned the visitors a deserved point at the death.
It meant that Alloa finished a point above the Blue Brazil despite their own 3-1 defeat by Falkirk.
Queens will host Falkirk in the first leg of the Premiership play-off quarter-final on Tuesday.
Meanwhile, the following evening, Cowden are away to Ayr United in the first leg of their Championship play-off semi-final.
Queens suffered a mighty blow when Reilly badly injured his ankle and will probably miss the play-offs.
Lineup, Bookings (0) & Substitutions (4)
Cowdenbeath
- 01 Flynn
- 14 Brett
- 02 McKeown
- 06 Wedderburn
- 05 Armstrong
- 23 Brownlie
- 26 Kane (Robertson - 67' )
- 04 O'Brien
- 21 Hemmings (Miller - 88' )
- 09 Stewart
- 18 Milne
Substitutes
- 03 Adamson
- 08 Stevenson
- 11 Morton
- 12 Gold
- 17 Usai
- 20 Miller
- 22 Robertson
Queen of the South
- 01 Clark
- 02 Hooper
- 03 Holt
- 08 Young
- 05 Dowie
- 06 Higgins
- 07 Kidd
- 04 Dzierzawski
- 09 McHugh
- 10 Carmichael
- 11 Russell (Reilly - 45' )
Substitutes
- 12 Atkinson
- 14 Reilly (Burns - 51' )
- 15 Burns
- 16 Kerr
- 17 McShane
- 18 Mitchell
- 19 Slattery
