After losing Adam Lyth cheaply, Ballance (55) and Andrew Gale (31) led the champions to 106-2 at lunch.
Steve Magoffin (2-33) removed Gale after the break and Ballance and Jonny Bairstow soon followed.
Jack Leaning (36) and Adil Rashid (53) added 72 for the seventh wicket after a rain delay, but Sussex reduced the hosts to 241-7 at stumps.
Needing to gain nine points from the game to guarantee survival in Division One, the visitors made a good start when England discard Lyth was trapped lbw for three by Chris Jordan in the fourth over.
Lewis Hatchett (2-47) picked up his first wicket when Alex Lees was given out leg before, but Gale and Ballance prevented any further damage before the interval.
As has so often happened in recent seasons, Magoffin was the man to break a partnership for Sussex, but Rashid and Leaning threatened to regain the initiative before Hatchett had Leaning caught at slip, and Chris Liddle (2-44) removed Rashid in the final over of the day.
Yorkshire have already secured their second successive County Championship title, having amassed a record 265 points this season.
Sussex dominated the first day against  Yorkshire to improve their hopes of retaining their Division One status.