The forward was unable to make a defining contribution to Germany's success in beating Argentina in the final - Mario Goetze would prove to be the extra-time hero - meaning the honour of finishing as the top goalscorer in this World Cup would remain with James Rodriguez.
The Colombian played only five matches and was knocked out in the quarter-finals, but his haul of six goals - including a spectacular volley against Uruguay - would prove to be enough. The Golden Boot has only been won four times by a player who also lifted the trophy, that statistic now preserved for another four years.
Mueller was the player in the best position to nick it away from Rodriguez ahead of last night's final to win his second Golden Boot in succession but couldn't deliver the solitary goal he needed to claim the award.
The 24-year-old was his usual whirl of perpetual motion in the German attack, playing largely on the right flank but also popping up centrally and on the left on occasion too as part of a fluid forward line.
As Germany dominated possession - in the first half of normal time especially - the Bayern Munich forward seemed more likely to provide an assist than add to the five goals he had scored earlier in the tournament, crossing for Andre Schuerrle, whose shot was well stopped.
He was unable to get a touch on a Philipp Lahm cross in the first half, then saw the ball fall at his feet in injury-time after Benedikt Hoewedes' header had cannoned against the post. In any case, he was offside on both occasions meaning any joy would have been short-lived. Mueller finishes on five goals for a second successive tournament, that tally not enough to take the award.
At just 24 years old and with the prospect of participating in a further two, possibly three, finals, he can at least console himself with the fact that, at this rate, he will surely go on to overhaul Miroslav Klose's newly-set record of 16 World Cup goals.
The only other realistic candidate for the award going into the final was Lionel Messi. The Barcelona forward began on four goals and, surprisingly, just one assist to his name, meaning he needed to either score a hat-trick or notch a brace with a couple of assists to take the award. In truth, he never really got close to either in an under-par performance.
The pre-tournament feeling that Messi would prove hugely influential in Argentina's march through the competition looked to be wholly accurate in the group stage when he scored four times, including a late, spectacular winner against Iran.
In the knock-out stages, however, he was unable to make his mark in the same way. Instead, it was the Argentine defence and goalkeeper Sergio Romero who would lead them to the final, keeping three pivotal clean sheets in succession to knock on the head the theory that Argentina were a one-man team.
If Diego Maradona is credited for virtually single-handedly earning the trophy in 1986, Messi was unable to do the same in 2014.
Messi , playing primarily on the right, was kept relatively quiet in the final as Germany dominated possession, but there were still opportunities for him to shine on the counter attack.
His finishing and passing, however, were unusually wayward and he couldn't lift his team-mates to better things.
His best chance to score came early in the second half, as he beat the German's offside trap to skip in behind Jerome Boateng.
A goal seemed inevitable, but Messi's left-foot shot squirted across Manuel Neuer and also beyond the far post. It was a difficult chance and he didn't miss by much, but it was the sort of opportunity you would normally expect him to bury.
He started to come into it more the longer the game went on, working another chance onto his left foot midway through the second half, but unable to bend his shot into the far corner.
There were a few other openings but Messi couldn't take advantage, either failing to find a team-mate with a pass or shut down by the German pairing of Mats Hummels and Hoewedes.
Messi had the beating of both in a foot race, but pace alone wasn't enough to make a telling difference on this occasion. Personal and team glory would once again evade Messi and Argentina.