Herrera provided a superb cross for Memphis Depay's opening goal at Vicarage Road but the playmaker lasted only 25 minutes, as a hamstring strain meant he had to be replaced by Marcos Rojo.
Jones was also substituted after the England defender twisted his ankle and United manager Louis van Gaal now expects both players to miss Wednesday's Champions League clash at home to PSV Eindhoven.
Watford looked like they had snatched a draw when Troy Deeney equalised with a late penalty but in injury time the striker went from hero to villain as his own goal gifted United victory.
United already have a lengthy list of absentees, including Wayne Rooney (illness), Anthony Martial (foot), Marouane Fellaini (calf), Michael Carrick (ankle), Antonio Valencia (foot) and Luke Shaw (leg)
Van Gaal also said striker James Wilson has a swollen knee
"We are in a lousy period because there are a lot of injuries," Van Gaal said.
"Jones and Herrera are not available for Wednesday
The first impression is they are not heavy injuries but we have to play Wednesday.
"Jones has a twisted ankle and Herrera maybe a hamstring injury
Rooney is ill and illness is a matter of days, not weeks.
"I do expect that he shall play Wednesday
He is at home
Tomorrow he comes and then I can say more.
"Martial has a foot problem
It is not so heavy as the media has written but you never know, we have to wait and see."
United's shortage of forward options offered an opportunity for Depay against Watford, who made his first league start since the 3-0 loss to Arsenal on October 4.
Depay's United career has been one of fits and starts since his £25million move in the summer and Van Gaal admitted this week he had expected more of the 21-year-old this season.
A lively display, however, was capped off by an excellent finish in the first half as Depay struck a sweet volley into the top corner to give United the lead.
"The goal was superb," Van Gaal said.
"A fantastic pass from Ander Herrera
He finished it very well
I think also the first half he played a very good game.
"The second half a little bit less, because he is six weeks out of the team and lacks some match rhythm so I can understand that.
"I think he played a very good match, like Jesse Lingard
The way we played, it suits them
That was good."
Watford were fortunate to be only one goal behind at half-time but the Hornets rallied in the second period and deserved their spot-kick after Rojo swiped through the back of Odion Ighalo.
Deeney slammed the penalty down the middle but five minutes later inadvertently restored United's lead after he bundled home Bastian Schweinsteiger's cross.
"It was painful to lose in extra-time because I think we deserved to draw," Watford head coach Quique Sanchez Flores said.
"In the second half we made a lot of effort to score
We scored in the last moment and felt it was possible to get a point against Man United - a very tough game - so to lose is very hard."
On Deeney, Sanchez Flores added: "It's a pity because as always he was very brave to accept the challenge to score the penalty.
"He scored it very well but it's Deeney - what happened is possible because he's fighting everywhere on the pitch, so he tried to remove the ball from the line of our goal.
"It's possible
It means Deeney is fighting in every moment in every part of the pitch
So we can take positive conclusions from it."
Source : PA
Source: PA