The errant header proved enough to secure all three points in an otherwise cagey affair that left Sam Allardyce & Co. four clear of the bottom three and took them up to 16th.
Two recent wins had already significantly reduced the pressure that had built on Palace, providing the momentum needed to eventually avoid relegation after a year-long decline.
Their manager had long spoken of the need to produce a run of positive results, but he has also frequently stressed he would accept draws amid occasional victories if they avoid defeat.
The way Palace started at Selhurst Park suggested he had told his team this was one of those occasions when a draw would suffice, but with Chelsea, Southampton, Arsenal and Leicester their next four fixtures they would have been taking a risk.
Allardyce made only one change to the team that won 2-0 at West Brom a fortnight ago, with Jeffrey Schlupp replacing the injured Patrick van Aanholt. The greater disruption may have come from them not playing since.
Watford's Daryl Janmaat and Craig Cathcart also came in for Stefano Okaka and Jose Holebas, but for the tedious opening 45 minutes there was little by way of a threat on goal.
Wilfried Zaha and Andros Townsend combined well to create space for the latter to cross to Mamadou Sakho in the 39th minute when Miguel Britos headed clear, shortly before Zaha struck over the crossbar. Then on the stroke of half-time, the visitors' Valon Behrami also volleyed high and wide from the edge of the area after the ball had fallen kindly to him.
Until Townsend's run down the right wing and cross in the 65th minute, neither Palace nor Watford came any closer. Younes Kaboul should have cleared the winger's delivery but it instead reached Zaha, who then created space amid pressure from Cathcart before again shooting harmlessly over.
It had by then become clear that one goal would likely secure victory for either team, and almost immediately afterwards Zaha took advantage of space on the left to make ground until being brought down by Britos.
From the resultant 69th-minute free-kick Yohan Cabaye sent an inswinging cross into the area, and at the near post - despite little pressure - Watford captain Deeney sent a powerful header beyond goalkeeper Heurelho Gomes' dive, beating him on his right.
Watford could no longer be content with the point that had been looking likely, but beyond a long-range strike from substitute Abdoulaye Doucoure that tested Wayne Hennessey, they offered little in response.
Benteke later hesitated when through on goal, allowing Kaboul to challenge him, and Zaha's pace on the left continued to create space, yet still a second score eluded the hosts.
In the end it mattered little. Victory took Palace to within three points of their 13th-placed visitors, who top the group at the bottom of the table that Allardyce has demanded Palace lead.