England’s Malan proved his worth as far more than a T20 specialist as the White Rose responded strongly to Sussex’s first-innings 313 on a true pitch.
They were bowled out for 558 after tea on day three, a lead of 245, before Sussex closed on 38 without loss from 23 overs in their second innings.
Malan was bowled by Irish off-spinner Jack Carson one run short of becoming Yorkshire’s first player to post double hundreds in two consecutive first-class innings having scored 219 in the Bob Willis Trophy last August.
Yorkshire started the day on 292 for two, trailing by 41, and they lost two wickets in each of the first two sessions and four after tea on the way to their highest total in five years.
Malan and Gary Ballance added only three to their overnight 177 third-wicket partnership - the latter caught behind off Jack Carson’s off-spin for 77.
Malan and Harry Brook then shared a high tempo 99, including 49 for Brook before he was caught behind down leg off the impressive seam of Jamie Atkins, who finished with a career best five for 98 from 26 overs.
That left Yorkshire at 374 for four, a lead of 161.
Dom Bess fell to Stuart Meaker shortly after lunch and Malan, having hit 22 fours and two sixes in 289 balls, fell for 199 for the second time in his career when Carson uprooted his off stump - 459 for six, a lead of 146.
The left-hander drove handsomely and deflected and guided serenely before being bowled by a turning delivery from highly rated Carson.
Nineteen-year-old wicketkeeper Harry Duke’s 54 - his second career fifty in his third Championship appearance - was supplemented by Jordan Thompson’s 42 as they took the home lead close to 250.
There was late cheer for Sussex seamer Atkins, also aged 19, as four of his wickets were taken on day three.
He claimed three of Yorkshire’s last four. He trapped Duke lbw, had Thompson caught at mid-off and bowled Ben Coad to wrap up the innings and begin Sussex’s bid for a draw.
A Yorkshire win would leave them four points behind Group Three leaders Lancashire following their defeat at Glamorgan.
But Sussex debutant Ali Orr and Tom Haines dug in impressively before close with 23 and 12 respectively.
Atkins said: “It was great to be out with the boys all day. I thought we stuck at it really well, and I was delighted to pick up five at the end. When Malan was past a hundred, it was almost like, ‘Where do I bowl to him?’
“We were trying to get him off strike for large parts of their innings. He’s a top quality batsman, and it’s a privilege to bowl to someone like him and Gary Ballance, players you grew up watching on TV. Tom and Ali were brilliant. It just takes so much pressure off everyone else that they’re still at the crease.”