Nabokov earned his fourth win of the season after denying an unchecked Jaromir Jagr from point-blank range during a Capitals' power play in the final seconds. Moments earlier, Jagr had a chance at the top of the crease but put a shot off both goalposts.
Patrick Marleau extended his goal-scoring streak to five games and added an assist for the Sharks, who improved to 11-3-1 in the last 15 meetings with Washington.
Marleau stuffed the puck past Olaf Kolzig during a two-man advantage, two minutes after his pass set up Teemu Selanne's team-leading 10th goal at 7:15 of the second period. Moments earlier, Marleau was denied on a breakaway by Kolzig.
Michael Nylander got the Capitals on the board 2:35 into the third period during another 5-on-3 power play. He got a perfect feed from Jagr during one of nine power plays surrendered by San Jose, which has given up seven goals while two men short this season.
Owen Nolan restored the Sharks' two-goal lead 6 1/2 minutes later on another power play, beating Kolzig to the short side from the edge of the slot.
Nylander and Peter Bondra set up Mike Grier's second goal of the season with 7:20 remaining.