Swede Elmander, signed for £10 million by former manager Gary Megson, was played clean through by Kevin Davies in the 87th minute only to steer his shot wide before Clattenburg ruled out Davies' 89th minute 'goal' from a corner for a push by the Bolton forward.
A drab first half only really came to life in its concluding five minutes as the home side finally carved out a couple of chances, both falling to midfielder Mark Davies.
In the 40th minute, Fabrice Muamba's shot was deflected into the path of Davies who failed to make clean contact on the ball and only succeeding in guiding the ball to Mark Schwarzer.
The closest the first half would come to a goal followed three minutes later with the same Bolton midfielder involved.
This time, Chung-Yong Lee's ball found the head of target man Kevin Davies who took advantage of Brede Hangeland's slip and nodded down for his namesake.
Mark Davies struck a fierce shot on target, forcing Schwarzer into a superb reflex block that turned the ball onto the bar.
Similarly, the second half took a long time to generate much interest, the arrival of Bolton substitute Vladimir Weiss, on loan from
Manchester City, providing a large impetus for the home team's attacking play, at least.
First, Tamir Cohen and Lee exchanged passes at the end of a flowing Bolton move, the former advancing and only being halted when Schwarzer saved at his feet. Then Slovakian winger Weiss cut in from the left for a crisp shot that deflected just over the Fulham goal.
Nicky Shorey's free kick for the visitors took a similar deflection over the Bolton crossbar and substitute Stefano Okaka steered a tame header at Jussi Jaaskelainen as the game continued in stalemate.