Mackail-Smith keeps Scotland hopes alive
Starting for the first time and winning his third cap, the striker headed over stranded home goalkeeper Peter Jehle to put his country on 11 points with one match against group winners Spain remaining on Tuesday.
The Czechs, who have 10 points, travel to Lithuania on Tuesday.
"We've got a good spirit, everyone wants to work for each other," Mackail-Smith told the BBC.
"It shows in how many chances we're creating and hopefully we can do that on Tuesday. We kept the ball well and if we can do that we stand a chance."
Should the two teams finish level on points the Czechs would earn a play-off berth due to their better head-to-head record in the two qualifiers against Scotland.