Smart, who had come on as a substitute in the first leg, was in the starting line-up for the second leg of the tie away against Wisla Krakow in Poland.
He looked lively on the left wing before being switched to the right as Skonto played defensively in their bid to frustrate their hosts, who had a 1-0 lead from the first leg last week.
But Wisla broke the deadlock soon after half-time after clever goal from Patryk Malecki, after which was Smart was taken off in the 55th minute.
Wisla went on to win the game 2-0 for a 3-0 aggregate triumph and play next week at Litex Lovech of Bulgaria in the third qualifying round.
Capetonian Cheyne Fowler came on as a second half substitute as his Finnish club HJK Helsinki notched up a record score by bearing Bangor City of Wales 10-0 in their second qualifying round tie.
HJK won 13-0 on aggregate and are now up against much tougher opponents in Dinamo Zagreb of Croatia.
Meanwhile, Bafana Bafana defender Morgan Gould started for Crystal Palace as they drew 0-0 with Wycome Wanderers in a pre-season friendly.
It is the final match for Gould during his trial at the club and he will now be hoping he has done enough to persuade coach Dougie Freedman before he returns to South Africa at the end of the week.