Hull City occupied second place prior to kickoff but the Tigers lost 4-1 at Bolton Wanderers, leaving the door open for Watford.
Jamie Ward ensured a nervous finish when he pulled one back for Derby, but Watford hung on for a crucial three points in their promotion push.
Ikechi Anya was also guilty of a glaring miss when he sliced wide after being picked out at the back post by a Vydra cross.
After seeing his teammates spurn golden opportunities, the Udinese loanee broke the deadlock with a run and powerful shot which went in off the post.
Poor Rams defending from an Almen Abdi corner allowed Ekstrand to bundle the ball into the bottom corner at the near post on 68 minutes.
Lloyd Doyley's challenge on Ward inside the penalty area gave Derby a route back into the match four minutes later.
The visiting forward stepped up to convert the penalty himself for his sixth goal in seven games, but it was not enough to prevent Watford from victory.