According to the official 2010 FIFA World Cup South Africa Regulations, the league format tiebreakers are as follows (article 17.6):
In the league format, the ranking in each group is determined as follows:
a) greatest number of points obtained in all group matches;
b) goal difference in all group matches;
c) greatest number of goals scored in all group matches. If two or more teams are equal on the basis of the above three criteria, their rankings will be determined as follows:
d) greatest number of points obtained in the group matches between the teams concerned;
e) goal difference resulting from the group matches between the teams concerned;
f) greater number of goals scored in all group matches between the teams concerned;
g) drawing of lots by the FIFA Organising Committee.
However, according to Ugandan website New Vision, these rules will only be applied in the third and final round of the qualifiers. For the second round, it seems the CAF tiebreaking rules (head-to-head results coming first) take precedence.
Here's the most interesting part of the article:
The table standings FIFA sent to the local football governing body FUFA indicate that Uganda are second in Group 3 , and will be among the teams considered as best runners-up after next week’s final round, if they beat Benin.