Emad Moteab headed home Egypt's crucial second goal five minutes into injury-time to leave both countries with identical records at the top of Group C in the African qualifying tournament.
Bougherra played the full 90 minutes on his first appearance since an international against Rwanda on October 11.
The 27-year-old has not played for Rangers since the 4-1 defeat by Sevilla on September 29.
He missed the 2-1 victory over Celtic and had to sit out another win at St Johnstone when he returned late from international duty after his passport was stolen.
Bougherra then suffered a knee injury in training and missed his club's subsequent five matches.
The former Charlton defender is now not due back to Murray Park until Friday and Smith admits the Clydesdale Bank Scottish Premier League clash with Kilmarnock at Ibrox may come too soon.
"It's one of those things we could have been doing without, and I dare say Madjid could be doing without it as well," Smith said of the play-off.
"I haven't heard yet how he has got through the game or if his injury has caused him any problems.
"We'll obviously have to see how he is, considering the fact he'll have been away nearly a fortnight.
"He has not played for two or three weeks prior to that. So, having two games in such a short space of time, having not played much, it might be asking a bit much of him to be involved in Saturday's game."
However, the Rangers manager is confident 17-year-old Danny Wilson will continue to prove an able deputy after impressing in his first three senior appearances.
"He has done very well indeed," Smith told Rangers World. "When a young player does get an opportunity, they are bound to to grab it.
"Danny was ready to show us what he can do. He was a bit unfortunate not to get a show slightly earlier in the season.
"Now he is in for the first time and he has played very well indeed."
Rangers played a behind-closed-doors game against Dundee United on Tuesday afternoon but Kirk Broadfoot was not involved following a slight hitch in his bid to return from an eight-month lay-off with a foot injury.
"Kirk started off last week coming back into training and then got a thigh strain," Smith said.
"It's natural when you have been out for so long that when you come back in you get niggling injuries. So we will just make sure he is okay before we re-start him again."
Meanwhile, the Rangers Supporters' Assembly have urged Dundee United to reconsider their decision to charge admission for the rearranged SPL fixture on December 15 - and threatened a boycott of future matches at Tannadice.
Supporters were told their ticket stubs would be valid after a waterlogged pitch forced the original game to be abandoned on November 1 but on Monday, United announced fans must pay £12, with concessions £6.
Assembly president Andy Kerr said: "We are absolutely astounded by Dundee United's decision to charge admission for the rearranged fixture.
"Rangers fans have already incurred expenditure for travel and admission for the original fixture and are being asked to do so again 10 days before Christmas.
"We feel very strongly that this is exploiting Rangers fans' loyalty and the initial reaction of many of our regular travelling fans and supporters clubs is that they will not attend the rearranged fixture and any subsequent fixtures at Tannadice.
"We feel we must make a stand on this issue as it is a stark example of taking advantage of Rangers fans. We strongly urge Dundee United to reconsider."
Rangers 1/4, Draw 9/2, Kilmarnock 10/1