Argentinian attacker Pereyra was once again Watford's inspiration, curling home a measured 20-yard finish in the 53rd minute to back up a sparkling opening-day brace against Brighton and Hove Albion.
Jose Holebas netted a fortuitous second 19 minutes from time as his cross from the left wing looped over goalkeeper Wayne Hennessey and into the far corner.
It meant Palace were unable to bounce back from Monday's 2-0 loss to Liverpool and the visitors were entitled to be aggrieved after Etienne Capoue was only booked for an ugly fourth-minute rake down Wilfried Zaha's ankle.
Zaha thankfully escaped unscathed and steered a shot through Ben Foster's legs in the 78th minute to set up a grandstand finish.
His team made the early running at a sodden Vicarage Road, although Christian Benteke's dwindling confidence was on show.
The Belgium striker sent a tame diving header wide before failing to direct a second effort downwards, allowing Foster to claw away.
At the start of the second half, Hennessey spread himself to make an eye-watering save at close quarters from Will Hughes.
The hosts were in the ascendancy by the time they took the lead. The sight of Zaha being dispossessed and Capoue driving forward to set up Pereyra's superb finish will undoubtedly have irked Roy Hodgson.
In the 70th minute, Benteke recovered some of the poise of old as brilliant chest control allowed him to whistle a shot just past the post. Holebas responded with far less precision but to much greater effect.
Zaha collected substitute Max Meyer's pass to become Palace's all-time Premier League top scorer and they should have claimed a point when Joel Ward planted a free header wide in the sixth minute of stoppage time.
24 - Wilfried Zaha is now Crystal Palace's top scorer in Premier League history (24), overtaking Chris Armstrong who netted 23 goals in the competition for the Eagles. Inspired. pic.twitter.com/pYKNcBZsH1— OptaJoe (@OptaJoe) August 26, 2018
What it means: Hornets flying high
Watford have won their first three games of a Premier League season for the first time and are only behind pacesetters Liverpool on goal difference. Meyer's lively cameo offered encouragement for Hodgson, given Zaha shoulders far too much of Palace's creative burden at present.
Pat on the back: Pereyra's purple patch continues
Few would have backed Watford's gifted Argentinian attacker be at the top of the Premier League scorers' charts at the end of August, but there he sits alongside countryman Sergio Aguero, former team-mate Richarlison and Sadio Mane. It was another marvellous finish from the 27-year-old and Vicarage Road came alive whenever he was on the ball.
Boot up the backside: Shameful moment for Capoue
The ex-Tottenham man put in a typically industrious performance in the Watford midfield, laying on the opener. But he should never have had the opportunity to do so after the sort of challenge that has no place on a football field.
Key Opta facts:
- This was Crystal Palace's first league defeat away at Watford since February 2009 (0-2 in a Championship meeting), having been unbeaten in seven trips prior to today (W3 D4).
- Watford have lost only one of their nine home games in the Premier League under Javi Gracia (W6 D2), including wins in each of their most recent three.
- Roberto Pereyra has been directly involved in seven of Watford's last 11 goals in the Premier League, scoring six and assisting another.
- Nine of Roberto Pereyra's 10 goals in the Premier League have been scored at Vicarage Road, including each of his last six in the competition.
A third Premier League defeat in succession at home to Southampton next weekend would paint a grim picture of what is to come for Hodgson's men, while Watford face a thorough examination of their lofty status against Tottenham. First up, the teams tackle respective midweek trips to Swansea City and Reading in the EFL Cup.