Clarke spent six weeks on compassionate leave following the loss of a close family member in February but his phased return helped Vale into the play-offs and they are now back in the third tier for the first time since 2017.
First-half headers by Harratt and Wilson put the Stoke club in control before former Stags ace Benning added the cherry on the cake with five minutes left to thump Nigel Clough’s 10 men, who had Oli Hawkins sent off in the 36th minute.
The two clubs endured roller-coaster seasons, with Mansfield going on a 12-game winless run early into the campaign while Vale won only one of their opening eight games before both outfits clicked ahead of the winter period.
With Nottingham Forest also set to visit the national stadium on Sunday, Stags boss Clough was hoping to start a double weekend of success for the family name and his side should have gone ahead.
Poor communication by Vale custodian Aidan Stone let in Jamie Murphy but he headed straight at the goalkeeper before the former Mansfield stopper had to head away a loose ball outside his goal with Rhys Oates closing him down.
By this point both sets of supporters had shown their support for Clarke with applause in the eighth minute started by the Stags fans due to that being the number he used to wear during his playing days at Field Mill.
Clarke in response applauded the fans of his current and old employers before he was able to punch the air in delight following the breakthrough goal in the 20th minute.
Harratt had been thwarted by the inside of the posts seconds earlier with half the stadium on their feet and he soon ensured the celebrations could begin.
Benning got away down the left and crossed in for the Huddersfield loanee, who stooped low and headed home to spark jubilant scenes in the Vale end.
Four minutes later and Clarke’s side were in dreamland. This time it was David Worrall crossing in from the opposite flank and although Ben Garrity’s header hit the crossbar, Wilson was on hand to nod in and make it 2-0.
Nathan Bishop stopped the advantage becoming three when he saved from Benning but Mansfield and Clough’s day soon went from bad to worse.
Hawkins, who had been booked for a needless push on Nathan Smith, went charging into Wilson by the halfway line and caught the Vale forward late. It left referee Jarred Gillett with no choice but to show a second yellow and subsequently a red card.
A further error by Stone almost opened the door for Mansfield to reduce the deficit before the break but while Oates fired under the goalkeeper, who had spilled a corner, Hall was able to get back on the line to clear in the nick of time.
Vale remained focused after half-time and only the offside flag initially denied Clarke’s men a third in front of 37,303 spectators at Wembley.
Harrart had the ball in the net after 64 minutes following a corner but it was ruled out before substitute Harry Charsley’s fine finish did not count because he had strayed a yard forward too early.
Mansfield continued to push for a lifeline and Stone denied Oates’ stinging drive before Vale put the game to bed.
Fittingly it was Benning who had the last word against his former club with a volley from Worrall’s centre to ensure a tearful Clarke could enjoy the final few minutes.