Craig Levein's side moved above Czech Republic into second place in Group I after Brighton and Hove Albion striker Mackail-Smith marked his first start for Scotland with a first-half header that was just enough to see off the the hosts in Vaduz.
The Scots, who now sit one point ahead of Czech Republic, lacked a cutting edge for long periods, but will face world champions Spain in their final qualifier on Tuesday knowing they will secure a play-off berth if they match the Czechs' result in Lithuania.
Spain are already through as group winners so Scotland may come up against under-motivated opposition in Alicante, but the quality of Vicente del Bosque's side still makes it a daunting assignment and a draw or defeat would be fatal if the Czechs win.
The Spaniards' 2-0 victory over the Czechs yesterday had reignited Scotland's dreams of snatching a play-off place and there was more good news before kick-off as Manchester United midfielder Darren Fletcher got the green light to captain the side after a quicker-than-expected recovery from tonsillitis.
Bright start for visitors
Scotland needed a stoppage-time goal from Stephen McManus to beat Liechtenstein when the sides met earlier in the qualifying campaign at Hampden Park. But they were on top in the early stages this time and Mackail-Smith - starting in the absence of injured Cardiff City striker Kenny Miller - appealed in vain for a penalty after being pushed by Rony Hanselmann.
Steven Naismith wasted two decent opportunities to open the scoring as the Rangers forward nodded wide from Fletcher's free-kick and then headed straight at Liechtenstein goalkeeper Peter Jehle from Barry Bannan's cross.
In between those two chances, Scotland goalkeeper Allan McGregor was called into action for the first time to push over Thomas Beck's long-range strike. Naismith miscued again when he looked sure to score after rounding Jehle but could only shoot into the side-netting.
Scotland search for second
Phil Bardsley tested Jehle with a powerful effort from distance before the opening goal that Scotland's pressure deserved finally arrived in the 32nd minute. Bardsley was the provider as he lofted a pass towards Mackail-Smith, who took advantage of poor positioning from Jehle to loop a header over the stranded goalkeeper into the empty net.
Scotland needed a second goal to end the hosts' hopes of snatching a surprise draw and Bardsley went close when he headed a Charlie Adam corner just over the bar at the near post. Christophe Berra's drive from the edge of the area brought a low save from Jehle, but Liechtenstein were able to keep the Scots at bay with relative ease.
Liechtenstein mounted a rare counter attack when Nicolas Hasler fired in a low drive which had McGregor scrambling to save at the far post. Jehle made good stops from Naismith and Berra in the closing stages but the Scots had done enough to take the priceless points.
Levein said: "We made it harder than it should have been. We had enough chances in the first half in particular to put the game to bed and of course when you don't get that second goal the opposition still have a degree of hope. But the way it worked out, I'm thrilled for the boys. We put ourselves in the position we wanted to get in this morning when we spoke about the match."