If you don't mind destroying the two input arrays then an easy way is:

use warnings;
use strict;

my @a = qw(0 1 5 7 9 5 3);
my @b = qw(a b c y e f z a a);
my @new;

while (@a && @b) {
    my $nextB = shift @b;

    if ($nextB =~ /[yz]/) {
        push @new, 'I';
    } else {
        push @new, shift @a;
    }
}

print "@new";
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Prints:

0 1 5 I 7 9 I 5 3
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If you don't like destroying the input arrays, make a copy first. If they are very large and copying them is not an option come back for a slightly uglier solution.

Update: actually it's not really uglier:

use warnings;
use strict;

my @a = qw(0 1 5 7 9 5 3);
my @b = qw(a b c y e f z a a);
my @new;
my $scanA = 0;

for my $nextB (@b) {
    if ($nextB =~ /[yz]/) {
        push @new, 'I';
    } else {
        last if $scanA >= @a;
        push @new, $a[$scanA++];
    }
}

print "@new";
[download]

Output is the same as above (of course).