Nabokov stopped 15 shots and Joe Pavelski scored twice in helping the Sharks down the Coyotes for the seventh straight time. San Jose won its fourth in a row with, Steve Bernier and Patrick Rissmiller each registering a goal and an assist.
Alexander Auld gave up three goals on 18 shots before being replaced by Mikael Tellqvist for Phoenix.
Jeremy Roenick scored the only goal San Jose needed with a slap shot that beat Auld over the left shoulder 4:21 into the first period.
Rissmiller made it 2-0 with his first goal of the season.