Hubbard connected off Matt Ginter to complete a four-RBI afternoon.
Chicago rallied for seven runs in the top of the eighth, tying it at 8-8 on a three-run blast by Paul Konerko.
Ray Lankford also hit a three-run shot for San Diego and RyanKlesko and Cesar Crespo smacked two-run homers.
Padres starter Bobby Jones pitched four innings, allowing one run and five hits with a walk and three strikeouts. Lefthander Cliff Bartosch was the victim in the eighth, yielding five runs and four hits while retiring just two batters.
None of the White Sox's three pitchers was effective. Starter Jon Garland was reached for five runs and seven hits in four innings, Jon Rauch surrendered three runs -- two earned -- in three innings and Ginter gave up three runs and five hits in the eighth.
Aaron Rowand had three hits, including a pair of homers, and three RBI for Chicago.