Liverpool started slowly and it took them 25 minutes to get in their first shot at goal. But the Merseysiders began to take over and Heskey warned of the dangers to come when he lashed a right-foot shot only inches wide.
Bolton had their moments, with Dean Holdsworth mis-kicking completely in front of goal after being set up by Ricardo Gardner.
Bolton continued to battle and were rewarded in the 54th minute when Holdsworth headed the ball on for Gardner to beat Liverpool keeper Jerzy Dudek.
Wanderers' substitute Ivan Campo then headed wide from a good position, but Liverpool were soon in front again when Baros grabbed his second in the 72nd minute firing home a Steven Gerrard cross.
It looked as if Bolton had earned a point in the 87th minute when a Kevin Nolan cross found Campo on the far post. The Spaniard chested the ball down before firing into the roof of the net.
But Bolton's brave fightback ended in the 88th minute when Heskey grabbed Liverpool's winner.
Liverpool manager Gerard Houllier said: "It was a tremendous performance beating a good team who are on a high. But after being pegged back twice we kept our heads high. I do not want to take anything away from Bolton but we deserved it."