The Bluebirds triumphed at Ninian Park, despite needing a Ross McCormack penalty in the seventh and final minute of added time to seal the points.
Watford had taken a 10th-minute lead through a Tommy Smith spot-kick only for Jay Bothroyd to level for the Bluebirds four minutes later.
"It was another late goal for us but it evens itself out over the season," said Jones.
"They kept breaking out after our set plays to cause us problems but we stuck to our principles and had our reward.
"We kept plugging away and we have players here who can change games and now it is all about results rather than performances.
"Watford played well but our central defenders were magnificent. The referee made the right decisions for both penalties and I'm only glad that ours proved to be the winner."
It was former Bluebird Jobi McAnuff's pace that led to the Hornets taking an early lead.
He outpaced Stephen McPhail down the left and cut into the area, where the former Leeds midfielder brought him down.
Leading scorer Smith slotted the penalty beyond the dive of Stuart Taylor who was making his home debut for the Bluebirds.
It took City only four minutes to equalise when a Chris Burke cross was not cleared by the visitors' defence and Bothroyd was in the right place to volley home.
Both sides attacked at every opportunity and defences had to be alert but it was Cardiff who went closest when first Bothroyd headed wide when well placed and then McCormack did the same after a flowing move.
Ninety minutes were up when McCormack fired in a shot that Watford keeper Scott Loach turned over the bar.
From the resulting corner, Roger Johnson headed goalwards and Watford's Ross Jenkins handled to set up City's grandstand finish.
Hornets manager Brendan Rodgers was bitterly disappointed that once again his side had suffered from a late penalty decision.
"I think it was a harsh result, particularly losing in such fashion," he said.
"The linesman said it wasn't a penalty which is why my players asked the referee to consult him. Ross Jenkins claims he never handled the ball.
"The performance level was very good, we have been excellent over the last couple of months but now we have to move on.
"To get so close yet lose was very disappointing as we still need points for safety but I will focus on the positives as you would have thought it was two top-six sides playing out there."
Watford are 16th in the table, five points above the relegation zone.