Having not dropped a set in two matches to reach third round, Murray and Williams were ultimately outdone by experience as Melichar and Soares – who reached both the Australian and French Open semi-finals together – battled to a 6-3 4-6 6-2 victory.
For Murray, the defeat brings his Grand Slam return an end to having lost at the second-round stage of the men’s doubles with Pierre-Hugues Herbert.
Williams meanwhile switches her attention to a semi-final against the unseeded Barbora Strycova on Thursday as the 37-year-old American targets a record-equalling 24th Grand Slam singles title.
Murray and Williams missed a break-point opportunity in the seventh game of the opening set and they were made to pay a game later.
On Williams’ serve, Soares – winner of five Grand Slam doubles titles including two with Murray’s brother Jamie – pounced with a fierce return before then finding the tramlines with to get the all-important break.
Melichar and Soares converted their first set point to take command of the match, but the second set continued to be a hard-fought affair as Murray and Williams sought to keep their doubles dream alive.
And with Soares serving to stay in the set, the Brazilian sent down two double faults to bring up three set points, and after saving the first, another double fault gifted Murray and Williams the set and took the match to a decider.
Soares and Melichar brushed off the disappointment to break immediately in the third set on Murray’s serve, and did so two games later on Williams’ to take a giant step towards the quarter-finals.
The top seeds kept their noses in front to book a spot in the last eight and pull the curtain and Murray’s doubles adventure at SW19.