The Lithuanians, who claimed their other win against the same opponents in Vaduz almost a year ago, improved their record to two wins and two draws from seven games.
The result lifted them into fourth place in Group C ahead of Baltic rivals Latvia, but any hopes of claiming a top-two place in the group had long gone.
Matulevicius slotted past Liechtenstein goalkeeper Peter Jehle in the 18th minute and Kijanskas headed home five minutes before the break to compete the hosts' win.
The result ends a recent improvement by Liechtenstein, which saw them claim draws in consecutive home qualifiers against Latvia and Slovakia before a narrow 1-0 home defeat to Greece last Friday.
Liechtenstein remain rooted to the bottom of the group with those two points from their eight games played.