The Germany captain grabbed his third goal of the season as second beat third at the Reebok Stadium.
Ballack's headed goal, which was scored late in first-half stoppage time, was the difference between the two sides.
But with United beating Everton at Old Trafford, Sir Alex Ferguson's side still sit pretty at the summit with a three-point advantage.
There was some debate over whether Ballack's goal was scored after time had passed in the first half. Abdoulaye Faye thought not and earned a yellow card for his complaints to referee Steve Bennett.
The goal stood, though, and the visitors gladly welcomed their half-time advantage.
But Bolton lacked a cutting thrust up front and Nicolas Anelka, playing as a lone striker, struggled to make his mark after a lack of supply.
Sam Allardyce's men, boosted by their 3-1 win over Arsenal at the weekend, started the brighter and had a chance to take the lead in only the third minute. Skipper Kevin Nolan headed over from a Nicky Hunt cross from the right as the home side looked to make the perfect start.
But then it was all Chelsea. Frank Lampard saw a 20-yard dipping drive parried by Bolton keeper Jussi Jasskelainen, before unleashing another fierce drive moments later. Jasskelainen parried again as Bolton felt the pressure.
In the 20th minute Didier Drogba saw his curling free-kick punched clear by Jasskelainen, before Lampard curled a corner in from the left and defender Ricardo Carvalho headed against the back post.
Michael Essien fired over as Chelsea pressed and then Geremi tried his luck with a long-range effort, but it was well wide of the target.
El-Hadji Diouf went close with a curling corner, which nearly caught Chelsea keeper Carlo Cudicini off-guard, but the Italian tipped the ball over the bar.
Andriy Shevchenko then showed a glimpse of his talent on an otherwise forgettable night. The Ukraine striker forced Jasskelainen to make a brilliant fingertip save from his 30-yard thunderbolt.
The pressure then told. Lampard's corner from the left found Ballack who, having lost marker Kevin Davies, glanced a powerful header past Jasskelainen at the near post.
Bolton rarely threatened in the second half, although their best chances fell to Tal Ben Haim. He fired agoninsingly wide three minutes after the resumption and then the impressive Diouf forced Cudicini to make a smart stop at point-blank range.
Bolton could have equalised in the third minute of stoppage time, but Cudicini saved well when Diouf got away a snap-shot from Jaaskelainen's hopeful long ball forward.