Dirk Kuyt's 49th strike for the club and Kevin Davies' own goal - either side of half-time - eventually proved enough in a performance which was lacking a touch of class if not endeavour.
Rafael Benitez's side are now unbeaten in six league games, in which they have conceded just once, and remain on course to deliver the manager's "guarantee" of Champions League football next season.
Wanderers were managing to crowd out Liverpool's tight passing game in and around the penalty area but when they did break free Emiliano Insua flashed a cross through the six-yard box with Kuyt just unable to reach.
The hosts were indebted to Sotirios Kyrgiakos for clearing Lee Chung-Yong's shot off the line after the South Korean's diagonal run from the right took him past both centre-backs and goalkeeper Jose Reina, making his 100th consecutive Premier League appearance.
Liverpool's pressure eventually paid off in the 37th minute with a move started by Albert Riera's inch-perfect crossfield pass to Insua on the left wing.
The Argentinian defender crossed to the far post where Alberto Aquilani jumped highest to head back into the six-yard area, and Kuyt stabbed home through Gary Cahill's legs.
Bolton thought they had won a penalty seconds before half-time when Lee tumbled in the penalty area under Aquilani's challenge but referee Steve Bennett booked the South Korean for diving.
Steven Gerrard tested Jussi Jaaskelainen with a driven 25-yard shot which the goalkeeper parried low to his right before the replacement of Aquilani with Lucas led to the second goal.
The Brazilian midfielder headed Riera's deep cross back for David Ngog to lay the ball off to Insua who drove in a shot which was heading wide until it deflected off Davies to wrong-foot Jaaskelainen.