At the Dubai Sports City Stadium, Scotland were dealt a blow in the morning before play began with captain Gordon Drummond pulling up with a rib injury and thus forcing himself off the field for the day. Scotland's 12th man Gordon Goudie stepped into the breach for the injured bowler who is hoping to be back for day three.
Medium-fast bowler Matthew Parker and off-break Majid Haq took the spoils for the Scots walking away with three-a-piece while Richie Berrington and Ross Lyons also proved useful with the ball.
Having dismissed Shabir Noori last night, Parker and Haq set to work on dismissing the top order and some tempting bowling by the duo along with Berrington saw Simon Smith snaffle four catches behind the stumps, including the key wicket of Afghan captain Nawroz Mangal for 56.
When the time came for the second innings, Fraser Watts started well only to see his opening partner, Preston Mommsen walk after being judged lbw by Samiullah Shinwari.
Things went from bad to worse after Kyle Coetzer was run out and yesterday's centurion Neil McCallum was out for a duck, caught behind off the bowling of Hamid Hassan.
The Scots were left battling in the afternoon sun on 65-6, a mere 105 innings lead, leaving things well poised for the coming days.
Scotland coach Peter Steindl said, ?It was a difficult start for us this morning with Gordon not being able to bowl but it was about bowling in the right areas today and showing discipline.
"I think in the first few overs of the morning we started a bit full, but about 45 minutes in we started to hit our straps and put the ball in the right areas and after lunch it was really good for the bowlers, Matty Parker in particular put in a long shift and kept asking questions and taking opportunities," said Steindl.
"I think we had a good start with the bat and at two down we started to let things get to us and we retreated into our shell. One bad over set us back but the thing for tomorrow is to get the lower -order to bat it out, get a good lead and then have our bowlers do what they did today," he added.
In regards to his captain's injury, Steindl was positive, "Gordon suffered an intercostal injury bowling yesterday in the second ball of his second over, it is tender but we're confident he'll be batting tomorrow, he got better as the day progressed and he'll also be having a bowl when the time comes."
Afghanistan's Shinwari said, "It was a good day for us as the captain and coach put me in to bowl and get the match back for us which I think I helped to do.
"I just think the spin worked for me today, I had to work a little but I managed to pitch it just right and the ball turned for the wicket. I hope that tomorrow I can take two more and make it five."