Ricky Rubio contributed 16 points and six assists for the Timberwolves, who won for the second time in four games.
Pekovic's foul shots with 14 seconds left put the T-Wolves ahead to stay at 96-95 and Andrei Kirilenko blocked two New Orleans shots over the final 6 seconds to seal the victory.
Pekovic finished with 13 points and six boards. Williams had seven rebounds.
Greivis Vasquez supplied 24 points, seven rebounds and five assists to lead the Hornets, who fell to 3-11 in their last 14 contests. Robin Lopez contributed 20 points and 11 boards for New Orleans.