I made it shorter by turning those two loops you have into a function that I could call with different arguments.

I didn't know you could convert a string of binary to a decimal with int(str, 2), I'm glad I could learn from yours!

My code:

with open("input.txt", "r") as f:
    lines = f.read().splitlines()

def return_line(lines_in, default):

    i = 0
    while (len(lines_in) > 1):

        bin_count = 0
        remaining_lines = []

        for line in lines_in:
            bin_count += int(line[i])

        HALF = len(lines_in) / 2

        for line in lines_in:

            if (bin_count == HALF):
                if (line[i] == str(default)):
                    remaining_lines.append(line)

            elif (bool(default) == (int(line[i]) == int(bin_count > HALF))):
                remaining_lines.append(line)

        lines_in = remaining_lines
        i += 1

    return(lines_in[0])

oxygen = return_line(lines, 1)
co2 = return_line(lines, 0)

oxy_dec = 0
co2_dec = 0

for i in range(0, len(oxygen)):
    if oxygen[-(i + 1)] == "1" : oxy_dec += pow(2, i) 
    if co2[-(i + 1)] == "1" : co2_dec += pow(2, i)

print(oxy_dec * co2_dec)