You haven't specified how the lines from the two files should match. I've presumed the first two columns should be the same:

my @file_one = (
    '1   100   5730_1 0.123',
    '1   200   5730_1 4.567',
    '21  400   5785_3 2.345',
);

my @file_two = (
    '1   100   1',
    '1   200   1',
    '21  400   60',
);

my %file2;
for my $line ( @file_two ) {
    my @f = split /\s+/, $line;
    $file2{$f[0]}{$f[1]} = $f[2];
}

for my $line ( @file_one ) {
    my @f = split /\s+/, $line;
    die "can't find match for $line"
      unless exists $file2{$f[0]}{$f[1]};

    print "$f[0] $f[1] $file2{$f[0]}{$f[1]} $f[3]\n";
}
[download]

Output:

1 100 1 0.123
1 200 1 4.567
21 400 60 2.345
[download]