The Welshman has picked up just one win in the league this season and further questions will be asked over his suitability for the role during the upcoming international break.
Manolo Gabbiadini's first goal of the season had looked like relieving the pressure on Hughes on Saturday, but Watford – enjoying their best start to a top-flight season – struck a decisive late blow.
Holebas' effort was deflected past Alex McCarthy to give the Hornets a share of the spoils and extend the Saints' winless run to eight league games.
Watford were punished for some early misses after 20 minutes when Danny Ings picked Roberto Pereyra's pocket from a corner, the loose ball falling to Gabbiadini to slide past Ben Foster from 12 yards.
Gerard Deulofeu was denied by McCarthy from an acute angle just after the half-hour mark before Foster made a superb stop with his foot to keep out Stuart Armstrong's low effort from 10 yards.
Watford should have had a penalty just before the hour when Nathaniel Chalobah was brought down inside the area by Ryan Bertrand, but Austin was convinced he had put the result beyond doubt 20 minutes from full-time, only for his deflected effort to be ruled out after Maya Yoshida – who made no contact with the ball – had strayed into an offside position.
The importance of that decision was brought into sharp focus eight minutes from time when Holebas' strike deflected past McCarthy off Cedric Soares to draw Watford level.
It could have been even worse for Southampton – and Hughes – but McCarthy's wayward punch from a corner bounced away to safety off the crossbar in the closing stages, meaning they remain outside the bottom three by virtue of goal difference.
What does it mean? Hughes under serious pressure
Southampton's dismissal of vice chairman Les Reed this week cranked the pressure up on Hughes. Failure to hold on for a second Premier League win of the season could mean the former Stoke City boss is no longer in the hot seat following the international break. Watford's impressive start to the season continues, meanwhile, and Javi Gracia will be disappointed they did not snatch all three points in the closing stages.
Gabbiadini grabs his chance
Making just his second Premier League start of the season, the 26-year-old showed a cool head to slot underneath Foster for what was so close to being the decisive goal for his side.
Deulofeu's wastefulness almost proves costly
He was lively in the opening stages but will rue two opportunities when he fired straight at McCarthy. Had he scored either, the Hornets could well have taken all three points back to Hertfordshire.
Key Opta Facts
- Southampton have lost just one of their last 11 matches against Watford in all competitions (W5 D5).
- Saints have failed to win any of their first six at home in a single league season in the top four tiers of English football for the first time.
- Watford have failed to keep a clean sheet in 11 of their last 12 Premier League away games.
- Manolo Gabbiadini scored his first Premier League goal at St. Mary's since October 2017 vs Newcastle, 391 days ago.
- Southampton's opening goal was their first in the Premier League that was not from the penalty spot in 615 minutes since Pierre-Emile Hojbjerg netted vs Brighton and Hove Albion in September.