Smith had managed meagre scores of 30 and three in two previous innings for the south coast side, who faced criticism for allowing the former Australia captain to adjust to local conditions ahead of next month's start of the Ashes series in England.
The ongoing County Championship match against Glamorgan at Hove is set to be the last of Smith's three appearances for Sussex before he joins up with Australia for their World Test Championship final against India at the Oval in early June.
A significant match in its own right, it is also Australia's lone 'tune-up' game before they begin their quest for a first Ashes series win in England since 2001.
Smith batted for nearly four hours for his 89 in the second division contest against Glamorgan.
But, in sight of three figures, Smith's 183-ball innings, including 10 fours and a six, ended when struck on the back pad by James Harris.
Umpire Martin Saggers raised his finger, with Smith seemingly upset by the lbw decision after possibly being outside the line.
But with no reviews in the Championship, Smith had no choice but to leave the field after resuming on his overnight 68 not out.
One of Sussex's arguments for signing Smith was that he would assist in the development of their young players and the home crowd did have a century to celebrate as teenager James Coles completed a maiden first-class hundred.
The 19-year-old's 138 was the centrepiece of Sussex's 481 all out -- a first-innings lead of 358 after Glamorgan were dismissed for just 123 with Smith's Australian teammate Marnus Labuschagne also dismissed leg-before to England bowler Ollie Robinson for one.
At the close on the second day of four, Labuschagne was 15 not out as the Welsh side were 118-1 in their second innings, still 240 runs adrift.
