How do I align tablenotes in a threeparttable

In the following example, I have used the flushleft option to the individual tablenotes environments. I have also embedded the tikzpicture in a tabular environment to overcome the alignment issue there.

\documentclass{memoir}
\usepackage{lmodern}            % Usa a fonte Latin Modern          
\usepackage[T1]{fontenc}        % Selecao de codigos de fonte.
\usepackage[utf8]{inputenc}     % Codificacao do documento (conv. auto. dos acentos)
\usepackage[brazil]{babel}
\usepackage[range-phrase={\,a\,}]{siunitx}
\sisetup{
    group-digits=true,
    group-four-digits=true,
    group-separator={\,},
    output-decimal-marker={,}
}
\usepackage{caption}
\captionsetup{
    justification=justified,
    %labelsep=quad,
    labelsep=endash, %% ABNT q manda
    position=above,
    skip=\onelineskip,
    width=0.95\linewidth,
}
\setfloatadjustment{table}{\centering}
\setfloatadjustment{figure}{\centering}
\setfloatadjustment{threeparttable}{\centering}
\usepackage{tikz}
\usepackage{pgfplots}
\usepackage[]{threeparttable}


\begin{document}        
\begin{figure}[]
    \caption{Pressão}
    \label{fig:pvapor2}
    \begin{threeparttable}
    \begin{tabular}{@{}c@{}}
        \begin{tikzpicture}[]
        \begin{axis}[grid=both,trim axis left, trim axis right,
        xlabel={Something else}, ylabel={Something},
        xmin= 1150,
        xmax=1550,
        ymin=-0.02
        ]
        \addplot+[ultra thick] coordinates { 
            (1300-273,101325*4.278*10^-11)
            (1400-273,101325*8.133*10^-10)
            (1500-273,101325*1.040*10^-8)
            (1600-273,101325*9.636*10^-8)
            (1687-273,101325*5.377*10^-7)
            (1700-273,101325*6.662*10^-7)
            (1800-273,101325*3.117*10^-6)
            (1900-273,101325*1.238*10^-5)
        };
        \end{axis}
        \end{tikzpicture}
        \end{tabular}
        \begin{tablenotes}[flushleft]
            \item Fonte: Autor.
        \end{tablenotes}
    \end{threeparttable}
\end{figure}

\begin{table}
    \caption{Planejamento}
    \label{tab:planejamentoexperimental}
    \begin{threeparttable}[t]
        \begin{tabular}{@{}SSSS @{}}
            \toprule
            \text{Ordem} & \text{Ensaio} & \text{Fator A} & \text{Fator B} \\
            \midrule
            12 & 1 & 0 & 0\\
            5 & 2 & -1.41421 & 0\\
            2 & 3 & 1 & -1\\
            11 & 4 & 0 & 0\\
            13 & 5 & 0 & 0\\
            10 & 6 & 0 & 0\\
            8 & 7 & 0 & 1.41421\\
            1 & 8 & -1 & -1\\
            9 & 9 & 0 & 0\\
            7 & 10 & 0 & -1.41421\\
            3 & 11 & -1 & 1\\
            4 & 12 & 1 & 1\\
            6 & 13 & 1.414214 & 0\\
            \bottomrule
        \end{tabular}
        \begin{tablenotes}[flushleft]
            \item Fonte: Autor.
        \end{tablenotes}
    \end{threeparttable}
\end{table}
\end{document}

Given that you're not using any \tnote directives, employing the threeparttable machinery and a tablenotes environment seems inappropriate or, at the least, like massive overkill. The simplest solution for your formatting objective would appear to consist of place the "Fonte" ("source", right?) line into the body of the tabular environment. In the code below, that's done by writing

\multicolumn{4}{@{}l}{\footnotesize Fonte: Autor.}

While you're making ajdustments, you should be a bit more deliberate in the way you use the S column type, especially in view of the fact that the SSSS one-size-fits-all approach is ill advised.

The same argument holds for the treatment of the material in the figure environment: There's no need for the threeparttable environment machinery. Just place the tikzpicture environment in a single-column tabular environment, with column type @{}l@{}, and let the second row consist of

\footnotesize Fonte: Autor. % second "row"

\documentclass{memoir}
\usepackage{lmodern}     % Usa a fonte Latin Modern          
\usepackage[T1]{fontenc} % Selecao de codigos de fonte.
\usepackage[utf8]{inputenc} 
\usepackage[brazil]{babel}
\usepackage{siunitx}
\sisetup{range-phrase={\,a\,},
         group-digits=true,
         group-four-digits=true,
         group-separator={\,},
         output-decimal-marker={,}
         }
\usepackage{caption}
\captionsetup{justification=justified,
              %labelsep=quad,
              labelsep=endash, %% ABNT q manda
              position=above,
              skip=1ex,
              %width=0.95\linewidth,
              }
\setfloatadjustment{table}{\centering}

\usepackage{tikz}
\usepackage{pgfplots}

\begin{document}        
\setcounter{chapter}{2} % just for this example

\begin{table}
    \caption{Planejamento}
    \label{tab:planejamentoexperimental}
    \begin{tabular}{@{} *{2}{S[table-format=2.0]}
                        *{2}{S[table-format=-1.5]} @{}}
    \toprule
    {Ordem} & {Ensaio} & {Fator A} & {Fator B} \\
    \midrule
    12 & 1 & 0 & 0\\
    5 & 2 & -1.41421 & 0\\
    2 & 3 & 1 & -1\\
    11 & 4 & 0 & 0\\
    13 & 5 & 0 & 0\\
    10 & 6 & 0 & 0\\
    8 & 7 & 0 & 1.41421\\
    1 & 8 & -1 & -1\\
    9 & 9 & 0 & 0\\
    7 & 10 & 0 & -1.41421\\
    3 & 11 & -1 & 1\\
    4 & 12 & 1 & 1\\
    6 & 13 & 1.414214 & 0\\
    \bottomrule
    \addlinespace
    \multicolumn{4}{@{}l}{\footnotesize Fonte: Autor.}
    \end{tabular}
\end{table}

\begin{figure}[h!]
    \centering
    \caption{Pressão}
    \label{fig:pvapor2}
    \begin{tabular}{@{}l@{}}
    \begin{tikzpicture}[]
    \begin{axis}[grid=both,trim axis left, trim axis right,
        xlabel={Something else}, ylabel={Something},
        xmin= 1150,
        xmax=1550,
        ymin=-0.02
        ]
        \addplot+[ultra thick] coordinates { 
            (1300-273,101325*4.278*10^-11)
            (1400-273,101325*8.133*10^-10)
            (1500-273,101325*1.040*10^-8)
            (1600-273,101325*9.636*10^-8)
            (1687-273,101325*5.377*10^-7)
            (1700-273,101325*6.662*10^-7)
            (1800-273,101325*3.117*10^-6)
            (1900-273,101325*1.238*10^-5)
        };
    \end{axis}
    \end{tikzpicture}\\ % end of first "row"
    \footnotesize Fonte: Autor. % second "row"
    \end{tabular}
\end{figure}
\end{document}