Their 1-0 defeat of Queensland Roar handed them the top spot over nearest rivals Adelaide United, who had a weekend off as they prepare for next Wednesday's AFC Champions' League final against Gamba Osaka.
Billy Celeski found striker Danny Allsopp off a corner and he flicked a header on to an unmarked Thompson for the only goal of the match to continue Queensland's nightmare home form this season. The defeat is the fourth in a row at home and equals the club's worst-ever home losing streak.
The fourth-placed Roar have bagged just one point from five home matches this season.
Sydney FC also missed out on a chance to keep up with Melbourne Victory when they went down 2-1 at home to Wellington Phoenix, courtesy of a late penalty. the capital side looked as if they might escape with a point after midfielder Stuart Musialik's speculative 30-metre (yard) shot in the 77th minute eluded Wellington goalkeeper Mark Paston after Leo Bertos had given Wellington an early lead.
Then striker Shane Smeltz was awarded a penalty in the 89th minute after Sydney defender Tony Popovic handled his cross. The former AFC Wimbledon man converted the penalty to claim his seventh goal of the season.
The win means Phoenix are off the bottom of the table and move above Perth and Newcastle into sixth spot.
Ivorian striker Eugene Dadi converted an injury-time penalty to earn Perth Glory a 2-2 home draw with Newcastle Jets on Sunday. The Jets led twice through Joel Griffiths and Tarek Elrich, but were pulled back, once by Nikita Rukavytsya and then again by Dadi's penalty after Argentine substitute Adrian Trinidad was brought down in the box.