How can I use Canvas upon/in/with Tkinter?

You are creating a canvas and a buttons frame. They are two different widgets and packed one after another. You can’t create any rectangle on top of the frame. So creating a rectangle in the canvas resizes the canvas widget that pushes the button's frame down.

You can create a canvas inside a button's frame and position using absolute positioning with the place command.

from tkinter import *
from functools import partial

colors = {
    0:"#ab91ff", 1:"#d0a176", 2:"#ecce86", 3:"#ecff91", 4:"#fff991", 5:"#92ff9f", 6:"#f991ff", 7:"#91dfff",
    8:"#d2ff91", 9:"#b8ff91"
}
buttonsPos = {
    "H":[1, 1, colors[0]], "He":[1, 18, colors[7]],

    "Li":[2, 1,  colors[1]], "Be":[2, 2, colors[2]], "B":[2, 13, colors[5]], "C":[2, 14, colors[0]], "N":[2, 15, colors[0]],
    "O":[2, 16, colors[0]], "F":[2, 17, colors[6]], "Ne":[2, 18, colors[7]],

    #more data...

}

DEFAULT_BOLD = ("Helvetica", "15", "bold")

class GUI():
    def __init__(self):
        self.root = Tk()
        self.root.geometry("900x414")
        self.root.title("Tabla periódica de los elementos")
        self.root.resizable(False, False)
        self.buttonsFrame = self.createFButtons()
        self.buttons = self.createButtons(self.buttonsFrame)

        self.c = Canvas(self.buttonsFrame, width=150, height=50)
        self.c.place(x=100, y=0)
        self.c.create_rectangle(0, 100, 150, 0, fill="pink")

    def do(self):
        pass

    def createButtons(self, frame):
        bs = []
        for k,v in buttonsPos.items():
            b = Button(frame, command=partial(self.do, str(k)), text=str(k), font=DEFAULT_BOLD, height=1, width=3,
                       borderwidth=4, bg=v[2])
            b.grid(row=v[0], column=v[1], sticky=NSEW)
            bs.append(b)
        return bs

    def createFButtons(self):
        frame = Frame(self.root, bg="#ebebeb")
        frame.pack(fill="both", expand="True")
        return frame

    def loop(self):
        self.root.mainloop()

if __name__ == "__main__":
    c = GUI()
    c.loop()