Ovechkin’s goal came after Washington tied the game with a short-handed goal by Nicklas Backstrom 49 seconds left in the third period.
The loss was the sixth straight for the Islanders and their 11th defeat in 13 games.
The goal was Ovechkin’s 21st of the season. Braden Holtby made 37 saves for the Capitals.
They appeared secure when Mike Green took an interference penalty at 18:50, but Backstrom slid the puck past Islanders goaltender Anders Nilsson for his sixth goal of the season to tie the score.
Aaron Volpatti’s goal at 8:58 of the middle period put Washington ahead 1-0. Tom Wilson and Martin Erat assisted on Volpatti’s second goal of the season.
Cal Clutterbuck’s short-handed breakaway goal at 3:59 of the third woke up the crowd at Nassau Coliseum. Clutterbuck broke in alone on Holtby and beat the goaltender to the glove side for his third goal of the season.
The Islanders have been on a spiral since beating Boston on Nov. 2 to move to 6-5-3
They are 2-11 since and 4-12 since they traded Matt Moulson and two draft picks to Buffalo for Vanek on Oct. 27.
The Islanders host Pittsburgh on Tuesday before a five-game trip against Western Conference teams. All five opponents on the trip are among the top seven teams in the conference.
The Capitals (14-11-2) won their second straight after a four-game losing streak.
The Caps are 17-5-3 against the Islanders since the start of the 2007-08 season, including their 6-2 over New York on Nov. 5 at Verizon Center.