He made an unbeaten 75 as the White Rose county stretched their lead to 388 by the close at North Marine Road.
Having bowled out the visitors for 94 to secure a first innings lead of 188, Yorkshire’s stand-in captain Ballance made the slightly surprising decision not to enforce the follow-on.
That allowed openers Alex Lees and Adam Lyth to play freely, with the former hitting Steven Mullaney for four successive fours early in the afternoon session.
The pair shared in a 72-run stand for the first wicket before Lees pushed forward to a Brett Hutton delivery and was adjudged LBW for 30.
Lyth followed shortly after having made 41, with an attempted flick into the leg-side landing back in the hands of bowler Luke Wood via a leading edge.
Those wickets saw the tempo of the Yorkshire innings drop somewhat, with Ballance and Jake Lehmann playing in a circumspect fashion as they took the lead past 300.
It was not until after tea that Lehmann looked to cut loose, but his innings ended on 35 as he miscued an attempted slog over mid-on off the bowling of Samit Patel which allowed Wood to take a steepling catch.
Jack Leaning also fell before close after being stumped off the bowling of Patel, leaving Ballance – who hit 12 fours in his 139-ball innings – and Tim Bresnan to see the hosts through to close, though play was abandoned seven overs early due to bad light.
Nottinghamshire had resumed on 38-2, but lost Michael Lumb without scoring as Ryan Sidebottom had him caught behind with a fine out-swinging delivery.
The former England seamer was at his devastating best, and dismissed both Steven Mullaney and Patel as he took three wickets in the space of 12 balls in the day’s opening half an hour.
Jack Brooks then followed his new ball partner’s lead by forcing Chris Read into a mistimed pull with just his fourth ball, allowing Lees to take a simple catch at cover, before having Brett Hutton caught at second slip by Lyth.
The procession continued as Brendan Taylor – who had been dropped when on nought – was bowled by Steven Patterson via an inside edge before Bresnan wrapped up the innings with the wickets of Wood and Luke Fletcher.
Nottinghamshire first-team coach, Wayne Noon, said: “We knew yesterday at 51 for six that we’d let them off the hook, but we didn’t realise we were going to be 94 all out.
“It’s not a 280 pitch and it’s definitely not a 90 pitch, so you’d say somewhere in the middle is par. It’s been a disappointing effort second half with the ball and definitely first half with the bat.
“We can’t feel sorry for ourselves – no one out there is going to feel sorry for us. It’s two weeks running that we’ve lost a wicket with the last ball or in the last over of a day’s play, and when you’re at the bottom don’t go your way.
“We are down in there but hopefully with a bit of weather tomorrow and a rearguard action with the bat we can fight for these five points then see where the next three games take us.
“We need a lot of weather and we need to hold our hands up. The top seven haven’t done it in recent times on flat wickets at Trent Bridge and now we’re going to have to do it on a wicket that’s seaming, bouncing and starting to spin a little bit as well.”