Midfielder Greg Halford's long throw from the right skimmed off the head of defender Chris Morgan.
Billy Sharp managed to pull the ball back from the line as the evergreen Gary Speed nipped in to finish from close range.
John-Joe O'Toole levelled matters in the 56th minute before Beattie - the club's top scorer last season with 22 goals - headed in the winner.
Minutes after carving out the opener, Halford picked out Danny Webber and the little striker swept wide to hammer in a low shot which Scott Loach claimed at the second attempt.
There was further misery for the injury-stricken Vicarage Road side in the 16th minute when Loach trudged off after injuring himself foiling Webber.
With first choice keeper Mart Poom out for six months with a dislocated shoulder, third choice Richard Lee took over.
Watford, who were dire for long periods, went close minutes before the break when Lionel Ainsworth fired wide with a spectacular overhead kick and centre-back Sam Sodje headed over.
They were back on level terms in the 56th minute when midfielder O'Toole headed in a Tommy Smith corner for his fifth of the season, before Beattie headed in a Sharp cross 10 minutes later.
Watford escaped in injury time with Speed and Sharp hitting the woodwork as United turned the screw.