The Scots headed into the match in Brussels sitting second bottom of Group A and still seeking a first win which was desperately needed to boost their slim hopes of reaching Brazil in 2014.
But second-half goals from Christian Benteke and Vincent Kompany just a minute apart meant the dramatic victory against one of the section favourites failed to materialise on another bitterly disappointing night for Scotland.
Levein made one change from the side who lost to Wales, with Wigan midfielder James McArthur drafted into the starting line-up in place of Scott Brown.
The Celtic skipper was forced to withdraw from the squad with an ongoing hip problem that forced him out of Friday's clash in Cardiff at half-time.
Injury to Marouane Fellaini should have been a boost for the Scots but they still faced a Belgian side packed full of talent in the shape of players such as Kompany and Thomas Vermaelen.
The home side were even in a position to name Eden Hazard on the bench, confirming speculation he would not start the game at the King Baudouin Stadium.
Belgium looked dangerous right from the first whistle and a Gary Caldwell error allowed Dries Mertens to burst into the box.
But goalkeeper Allan McGregor came to the rescue and blocked superbly at both attempts by Mertens to deny the home side the opener early on.
Fortunately for the Scots, McGregor was on top form and he also saved well from Nacer Chadli at the near post before diving bravely to the feet of the same player to snuff out another threat.
After a period of intense pressure from the Belgians, a mis-hit shot from James Morrison caused more problems than it should have for Thibaut Courtois.
The goalkeeper looked more convincing when he prevented a curling free-kick from Shaun Maloney from finding the top corner after Kris Commons was fouled just outside the box by Moussa Dembele.
At the other end, Chadli was given enough space to unleash a thunderous strike from 25 yards that whistled inches past the post, before Dembele and Mertens both saw efforts fall wide of target.
With half-time approaching, Scotland threatened from another free-kick, with Commons forcing a decent save from the keeper on this occasion.
Both sides made a change at the interval, with Jamie Mackie replacing Commons and Dembele making way for Hazard.
The Belgians hit the woodwork within five minutes of the restart when Benteke threw himself in front of Toby Alderweireld's cross only to see his header clip the crossbar on the way over.
Kevin Mirallas was thrown into the action for Mertens, before McGregor was shown the first yellow card of the game for time wasting on the hour mark.
The breakthrough came for the Belgians after 69 minutes when Benteke bulleted home a header at the back post, eventually beating the impressive McGregor.
Belgium doubled their lead a minute later when Kompany collected from Hazard on the edge of the area and rifled an unstoppable shot into the back of the net.
It was a crushing blow for the Scots, who replaced Steven Fletcher with Kenny Miller, with just over 15 minutes to go.
Blackpool's Matt Phillips was then handed his competitive debut, confirming his allegiance to a Scotland side whose slim hopes of reaching the World Cup finals were, by then, left in tatters.