Fowler struck seconds before the break to secure the points against a defiant Bolton on his 31st birthday.
And his all-round play will give Benitez plenty of food for thought as he plans for the future.
Fowler knows the Spanish coach could bring in a couple of bright young strikers this summer which would probably end his second spell at the club.
But he clearly will not go quietly and showed their is life in the old dog yet.
Steven Gerrard's return to midfield after suspension was Liverpool's only change from the side that won at West Brom last time out while Djibril Cisse held his place on the right.
Bolton had Nicky Hunt at full-back in place of the injured Joey O'Brien in their only change from the side that last at Birmingham.
And they started brightly and could easily have had a couple of goals inside eight minutes.
First Bruno N'Gotty's free-kick reached Kevin Nolan in the six yard box, but his attempted clip over Jose Reina was held by the Spanish 'keeper.
Then a deflection off Abdoulaye Faye sent Stelios Giannakopoulos through the middle, but this time Reina made a much more difficult save to his right when the Greek star should really have finished better.
Liverpool were constantly on the back foot as Bolton pressed and harrassed at every turn, producing good possession and movement.
But the Anfield crowd's frustration was compounded when Fowler was given offside while taking possession of a throw in - Benitez was equally enraged.
It was painfully slow progress for Liverpool against Bolton's efficient organisation. John Arne Riise saw a 25 yarder drift wide before producing the left wing cross that dropped for Harry Kewell, the Aussie hooking over from 12 yards.
N'Gotty, Tal Ben Haim and Faye were a formidable triangle of defence that Peter Crouch found hard to overcome, while at the other end Liverpool frequently failed to deal with the 'second ball' in the box as Kevin Davies and Nolan caused plenty of problems.
Gerrard failed to win a penalty when he went down under the combined attention of Ben Haim and Gary Speed, with Kewell seeing a cross-shot flash wide and Jussi Jaaskelainen punching away a Gerrard free-kick.
But Liverpool did maintain pressure in Bolton's last third near the break and a Crouch header saw Jaaskelainen save low down following a Gerrard corner.
Seconds from the break Fowler buried a 12-yard chance after winning the initial header and then feeding off Crouch's touch down. It was a scoreline Bolton hardly deserved.
The obvious need for more guile from Liverpool's attacks saw Luis Garcia on in the second half in place of Cisse. Immediately the Spaniard went close with a header.
Then Xabi Alonso cracked an 18 yarder against the foot of a post after outstanding work down the left by Gerrard and Fowler. Bolton replaced Giannakopoulos with Henrik Pedersen seconds after.
Sami Hyypia was then booked for a late tackle on Ricardo Gardner before Matt Jansen replaced Jay-Jay Okocha.
Crouch, though, continued to have one of those games when little went right and his only use was as a disruptive influence. He wasted a good opportunity created by Kewell with a weak header.
Ivan Campo replaced Faye before Dietmar Hamann took over from Fowler, who fully deserved his ovation from the home crowd.
Kewell ran from half way, being tugged by Hunt all the way, before firing wide of the far post, Liverpool striving for the second goal that would end the contest.
But Bolton worked tirelessly to get something from the game and it was anything but easy for Liverpool.
Djimi Traore coming on for Kewell two minutes from the end underlined Benitez's desire to defend rather than increase the lead.
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