Following up Friday's draw in Lithuania, the hosts took 36 minutes to break the deadlock when Sapara swept home a cross from the right by Vladimir Weiss.
Marek Hamsik headed just over the bar two minutes later as Slovakia looked for a second, but the visitors held out until after the break, when Weiss hit a long-range effort over the bar.
Weiss flashed another shot wide and Martin Skrtel missed the target from 12 yards before the hosts finally made the game safe with their second goal after 77 minutes.
Miroslav Stoch hit an initial shot from 12 yards which was picked up by Jakubko who placed it right-footed into the bottom corner of the net.
Stoch could have made it three when he fired straight at visiting goalkeeper Peter Jehle in the dying minutes, and Jakubko also came close again in injury time.