Paul Parry (44), Kevin McNaughton (49) and Joe Ledley (63) scored the goals that saw the Bluebirds finish the season in the top half of the Coca-Cola Championship.
"It was good to finish with a big victory in front of our own fans," said Jones.
"It was always going to be a mental test for the players, but they have all come through very well.
"We are all disappointed that we haven't finished in the play-offs, but we are growing as a club and there are good foundations here now."
City showed only one change from the team that beat Barnsley at Wembley, with leading scorer Parry up front in place of Steve Thompson.
The Bluebirds set the early pace and Jimmy Floyd Hasselbaink twice went close before Peter Whittingham rattled the crossbar with an angled drive.
Parry's all-important opener came a minute before the interval following a dazzling run by Glenn Loovens.
He switched to Ledley and the hero of Wembley laid the ball back to Parry, who drilled home a low shot for his 11th goal of the season.
The game was put beyond the Tykes four minutes into the second half. McNaughton found himself on the byline and chipped over Luke Steele, and the ball had crossed the line before Ledley rushed in to make sure.
It was Ledley who claimed the third following a mistake by Dennis Souza. He failed to clear under pressure and Ledley was left with the simple task of side-footing beyond Steele and into the far corner.
Despite the defeat, Barnsley boss Simon Davey still believes it has been a good season for his club.
"It has been a long, hard season for us all, but we can look at victories over Liverpool and Chelsea, as well as being very competitive in the league," he said.
"The Championship is a fantastic division to be in and that is why we have worked so hard to stay there.
"I wish Cardiff City well in the cup final, and it is a tribute to the Championship that we had three teams in the semis."
Cardiff can now look forward to their preparations for Wembley in good heart.
"I have a team in my head for the final but I will be watching Portsmouth next week and if I need to change my way of thinking then I will," said Jones.
"The next 10 days could also give Robbie Fowler the opportunity of upping his training and pushing his way into the squad."
Sporting Life.