The White Rose county were bowled out for 249 just before the close after initially getting into a promising position thanks to a century partnership between the Australian and captain Andrew Gale.
At one stage midway through the afternoon, Yorkshire were 148-2 with Gale unbeaten on 38 and Jaques 75.
However, Jaques being run out by a direct hit from Lee Daggett and the subsequent dismissal of Gale just five balls later triggered a collapse that meant they were able to claim just one bonus point.
With Northamptonshire due to start their reply at 11am, the second day promises to be an intriguing affair and Jaques, for one, insists Yorkshire are very much still in the game.
He said: “It was disappointing as we worked really hard in the morning to set things up.
“We got through that but then we were unable to go on and cash in. There has been a bit of soul-searching going on. A lot have gone away and thinking about those shots. They would like to have them back. But these things happen.
“Now, we have to regroup and come back in the morning and put the ball in the right areas.
“They did that and if we can do the same then there is enough going on with the wicket to make things happen.”
Jaques had a spell at Northamptonshire earlier in his career so knows better than most what to expect from the Wantage Road wicket in the next three days. He added: “I believe we will get a bit more up and down action. It was a bit two paced and that will only increase.
“Maybe it will get a bit lower and slower but some (deliveries) are bouncing up as well. Adam Lyth got one. He was looking to get forward but it hit the grip on his bat.
“Galey, too, got one that hit his bat high up, while I had six or seven of them. I think we have batted on the best of the wicket. It will still be decent (today) but then, hopefully, it will be playing up a bit in the last two days.”
On the state of the game ahead of Northamptonshire’s reply getting under way, Jaques said: “You want to go big in the first innings and put the pressure on. But the game is moving forward with 10 wickets having gone down on the opening day.
“Northamptonshire bowled well and put the pressure on.”
Ryan Sidebottom will step up his recovery following a calf tear by playing for the second team next week before, hopefully, making a return ahead of the Championship clash with Derbyshire on August 15.