The league champions stormed into a 3-0 first half lead at AFC Stubbington before the hosts replied just before the interval.
Meon’s stand-in keeper, Adam Beckett, was sent off after the restart for dissent - meaning midfielder Bill Cook had to don the gloves.
Stubbington, who had lost 2-0 and 3-0 to Meon in MSL games in 2020/21, pulled another goal back and equalised 15 minutes from time.
There was a dramatic finale with Meon awarded a late spot-kick for handball and Whitcombe coolly converting his second goal.
We went 3-0 up through Jagjit Singh, an OG from a corner supplied by Dan Edwards and Bayley whitcombe. They then scored before half time 1-3 HT.
Meon will now face league runners-up Mob Albion in the final at Front Lawn on June 19 (3pm).
Darren Ferguson hit a hat-trick as Mob caned Burrfields 5-1 in their semi-final.
Top scorer Harry Potter and Cam Palin were also on target.
Stubbington, who had lost 2-0 and 3-0 to Meon in MSL games in 2020/21, pulled another goal back and equalised 15 minutes from time.
6. A Stubbington opponent lunges into a tackle on Meon's Bayley Whitcombe
Chris Moorhouse Photo: -
8. Bayley Whitcombe scores Meon Milton's late penalty winner against Stubbington
Kevin Shipp Photo: -