The result meant Sheffield finished third from bottom, three points above Frickley, while Colls ended in 12th.
It was a disappointing finish for the Ponte team who have had an up and down campaign, but have also been encouraged with plenty to build on for next term.
They found themselves one down after 23 minutes when Josh Burns headed home from a corner.
Mikey Dunn levelled with a smart lob over former Ponte keeper Ryan Musselwhite just past the hour mark, but within six minutes the visitors were back ahead as Rory Coleman found the net with a superb curling free-kick.
“A good old fashioned non-league game to finish with two sides going at each other well and a goal worthy of winning any game at any level,” said Colls manager Craig Rouse.
“Another crazy season over and done with. Loads of ups and downs, lessons learnt and positives to take forward.
“The planning starts now for next season as we look to improve on and off the pitch.
“As all managers know there’s never any rest period. Well done to all players, staff and volunteers, it’s been a long old slog especially after the two covid seasons.”
Colls defender Spencer Clark, meanwhile, is the latest player to commit to the club by signing a new deal for the 2022-23 season.