Troy Deeney scored twice for the Hornets while Mark Yeates and Matej Vydra were also on target and despite Marcus Tudgay scoring a consolation effort in stoppage-time, Watford were always in control.
"It's been a little bit of rock and roll for us today but in the end the final was perfect," said Zola.
"I'm delighted with the result, very pleased for the players but it's been hard. I don't think the result is too fair towards Barnsley because they played a good game. Yes, probably we deserved to win but not in that way.
"We had some very good chances, great chances and we didn't manage to take those opportunities and in the end they could have got a draw.
"They played well, they created some very good chances and I think if it wasn't for Manuel Almunia today I think the first half could have been 1-1.
"In the second half we didn't start very well, they pressed us in our box but the second goal changed the game completely.
"It really killed them and from that moment there was only one team on the pitch."
The victory takes Watford into the promotion places in the Championship and the Italian admitted he would be delighted if they could remain there.
"I would like to have that place at the end of the season," he added.
"Obviously we are delighted, there's a good atmosphere at the ground with the players and with the supporters but we need to make sure we keep the balance.
"There's a long, long way to go and in the Championship you cannot afford to lose concentration."