Slovenia finished third in the section on 16 points from 10 games, behind winners England and second-placed Switzerland who qualified automatically for next year's tournament in France.
Needing only a draw to avoid any possibility of a last-minute fiasco, Slovenia produced a largely tepid performance against the group's bottom team.
They failed to trouble San Marino's packed defence in the first half and nearly fell behind after the home side's 39-year-old skipper Andy Selva shot wide from close range.
Substitutes Pecnik and Tim Matavz injected a little more urgency into Slovenia's attacks after the break and Cesar finally broke the deadlock in the 54th minute.
The towering central defender was left unmarked on the edge of the box to turn an Andraz Kirm corner past keeper Aldo Simoncini.
Pecnik added the second with a powerful header from 10 metres which shaved the inside of the near post after a sharp cross by left back Bojan Jokic.
Pecnik missed the game's final chance in added time when he failed to get on the end of an inviting cross from the left by Dejan Lazarevic.
(Writing by Zoran Milosavljevic in Belgrade; editing by Ken Ferris)
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