Smith fell eight runs short of his third consecutive hundred as he was trapped in front by Chris Woakes on 92 from 161 deliveries in which he hit 14 boundaries.
Australia, who were tottering at 102/5 at one stage in reply to England's first innings score of 258, were bowled out for 250 with Stuart Broad returning best figures of 4/65.
Woakes took three wickets for 61 runs and Archer grabbed two giving away 59 as England once again got past the entire Aussie batting except Smith who seemed to be in a league of his own.
A mean Archer bouncer sent Smith reeling to the ground, threatening to cut short a masterclass knock as the ace batsman was forced to retire after lunch.
Smith was batting on 80 from 152 balls when in the 77th over a delivery by Archer hit him on the unprotected part of the neck. The medics ran into the middle from both sides, as the England players rushed to the former Aussie skipper immediately.
As Smith lay on his back before slowly getting back on his feet, he looked dazed. The medics forced him to leave the field with Australia at 203/6, still some way behind England's first innings score of 258.
Smith walked back to the pavilion to loud applause after helping his side out of a hole as he did in the first Test. At the crease were Pat Cummins with Peter Siddle joining him.
Soon Smith, who at the outset did not want to leave the field, walked back but this time he was not as composed as he was before the knock, leaving a straight delivery from Woakes which hit his pads and he was plumb.
Smith started walking only to stop for a desperate review which did not help his cause. Cummins fought hard for his 20 off 80 balls (3x4) as the Aussies fell eight runs short of England's total, which at one stage looked impossible.
Earlier, skipper Tim Paine was out for 23 just after lunch, Archer removing him. Archer then bowled an inspired spell of fast bowling few can match at this level to even trouble Smith.
Nathan Lyon scored 6 while Josh Hazlewood remained not out on 3. This was Smith's seventh consecutive Ashes knock of 50-plus, a record he now holds outright after bettering Mike Hussey's achievement of passing 50 in six straight digs against England.
Brief scores: 1st innings: England 258 all out (Rory Burns 53, Jonny Bairstow 52; Josh Hazlewood 3/58, Pat Cummins 3/61, Nathan Lyon 3/68); Australia: 250 all out (Steve Smith 92, Stuart Broad 4/65) At Tea.
( With inputs from IANS )