Gordon Strachan's much-changed side held out at the Karadjorje Stadium until the break but a second-half double by Heerenveen striker Filip Duricic gave the home side a deserved win.
Scotland remain bottom of Group A with two points from six games ahead of the trip to Croatia in June and on this evidence there is little chance of the first section win arriving.
It was another dismal night for the Scots.
The 1200 or so Tartan Army supporters who made the trip to Serbia, some of whom had helped clear snow off the pitch in the afternoon to allow the game to go ahead, saw several different faces from the side who lost 2-1 to Wales at Hampden Park on Friday night.
George Boyd, on loan at Hull City from Peterborough, and Brighton's Liam Bridcutt, were handed debuts as David Marshall was given a rare game in goal at the expense of Allan McGregor.
Defender Steven Whittaker, midfielder Steven Naismith and striker Jordan Rhodes came into the starting line-up as the Scots looked for their first Group A win at the sixth time of asking.
The setting, however, was less than inspiring.
There was a poor crowd inside a rather ramshackle 12,000-capacity ground on a sodden Serbian evening with both sides having little more than pride to play for at the halfway point of their respective campaigns.
The whole Serbia squad and backroom team went into a huddle before the game in a show of solidarity and it certainly drove them on for most of the game.
There was only 30 seconds gone when Marshall had to make a save from lively striker Duricic after skipper Branislav Ivanovic, playing all over the pitch it seemed at times, had sent him through on goal.
The visitors defended two corners in the first three minutes and while they worked their way into the game on a bog of a surface, Marshall was called into action again in the ninth minute when he had to get down smartly to his near post to save a low drive from Dusan Basta.
Scotland were living dangerously, too often at the edge of their own penalty area.
In the 20th minute though, after they had pushed further up the park, Duricic took a long ball from the back and skipped past Scotland stopper Grant Hanley with some ease but Marshall was again equal to the task, diving low to block the drive.
Serbia midfielder Zoran Tosic fired a drive from 20 yards just past Marshall's left-hand post with 27 minutes gone, as the Scots survived another attack.
Charlie Adam replaced James McArthur for the start of the second half.
In the 48th minute Naismith had the ball in the net with a lovely curling shot from the edge of the box but the flag was up for offside.
At the other end Duricic went down in the box after a challenge by Hanley but Hungarian referee Istvan Vad was unimpressed with the claims for a penalty.
Marshall looked confident in holding a powerful drive from Serbia midfielder Ljubomir Fejsa but the game was drifting into something of a stalemate.
In the 59th minute the Scots were handed a great chance when Serbia defender Neven Subotic took a fresh air swipe at the edge of the box giving Rhodes a clear look at goal but the Blackburn Rovers striker's effort was powder puff and fell into the arms of Vladimir Stojkovic.
Serbia promptly ran up the other end and scored.
Tosic crossed from the left to Fejsa whose shot was blocked and when it fell to Duricic, he spun and slammed the ball into the net from around six yards.
Five minutes later the home side doubled their lead when Gary Caldwell tried to pass the ball out from a dangerous position instead of playing it safe. Nenad Tomovic got in front of Alan Hutton to intercept and although Marshall saved his shot after the defender had evaded Hanley, the ball broke to Duricic to slide into the empty net.
Rhodes had a half-chance a few minutes later after good work by Bridcutt, but could not get his shot away on time.
In the 80th minute Chris Burke replaced Shaun Maloney and Kenny Miller came on for Rhodes but the game petered out to another dark blue disappointment, although there was time for Ivanovic to miss the target from close range after the visiting defence had been carved open again.