Michy Batshuayi looked to have salvaged a point for Chelsea but it was fellow substitute Cesar Azpilicueta who broke Watford hearts in the 3-2 win at Stamford Bridge.
The hosts took the lead in the 12th minute when Pedro wrapped his foot around a stunning 25-yard effort to give Chelsea the initiative.
But Abdoulaye Doucoure was out to spoil the party when he equalised in time-added-on before the break, lashing home a volley to level things up.
And Pereyra was the man who dealt what appeared to be the crucial blow when some lax defending allowed the Argentine acres of space in the box before he slotted past a helpless Thibaut Courtois in the Chelsea goal.