The French international forward showed glimpses of the form that has convinced managers to pay more than £50 million in total transfer fees for his services over a seven-club career.
But he was hauled off after 70 minutes by new boss Sam Allardyce and Bolton had run out of ideas by the time defender Shittu needlessly hacked at substitute Idan Tal in the 94th minute, presenting Gary Speed with the chance to convert the only goal of the game from the penalty spot.
It was rough justice on the visitors who should have wrapped up their first away points of the season well before then.
In the 20th minute, a mistake by Quinton Fortune presented Darius Henderson with the chance to head the ball goalwards sparking a furious scramble.
The ball broke to Damien Francis whose shot struck the foot of Jussi Jaaskelainen's left-hand post with the rebound ricocheting to Ashley Young whose driven strike flew just wide of the target.
That was the low point of a poor opening to the game by Allardyce's team who clearly struggled to accommodate Anelka in their tried and trusted three-man forward formation.
After 35 minutes, Allardyce had seen enough and hauled off out-of-sorts right-back Nicky Hunt, reverting to a 4-4-2 formation with substitute Ricardo Vaz Te playing on the right wing.
That switch brought an improvement in Bolton's play but the home side, impressive 2-0 conquerors of fancied Spurs on the opening day of the campaign, could still come no closer to a goal than a superb effort from Anelka just before the hour.
There seemed little immediate danger as he gathered the ball on the edge of the Watford area fenced in by yellow shirts but, a couple of twists and turns later, he had made space for himself and unleashed a thunderous 20-yard drive that was parried well by keeper Ben Foster.
In the first half Anelka had shown comparable skill when Ivan Campo's threaded through ball found the Frenchman who curled a shot wide of the Watford goal.
Those moments of skill were enough to assure Anelka a resounding cheer from his new supporters when he was eventually brought off by Allardyce 20 minutes from time.
But there was no doubt that this was, by their high standards of recent seasons, an extremely disappointing showing and one which suggested that Allardyce and his team will have to work hard on the training ground to integrate their new star into their team.
The damage could have been a lot worse if Watford had enjoyed slightly more luck and composure in front of goal.
Henderson missed a good opening in the 59th minute when he rose and headed just over from Young's far-post corner.
And in the final 10 minutes before the penalty, Watford should have taken a lead.
First Young showed great skill inside the box to find room for himself and curl in a shot which beat Jaaskelainen but rebounded to safety off the bar, then Marlon King fired just wide in injury-time and with their last chance of the game Malky Mackay also headed against the bar.