use awk:

awk '/^>/ { printf(">Seq%d\n",(++i)); next;} { print }' < input.fa > output.fa

Ex:

echo ">fastsdde135667667
actgcagtctga
>fgdte12875
actggact" | awk '/^>/ { printf(">Seq%d\n",(++i)); next;} { print }'

>Seq1
actgcagtctga
>Seq2
actggact

also, this:

#!/usr/bin/perl

$count =1;

while (<>){
        if (s/^>.*/>Seq$count/){;
        $count++;
        }
        print;
}

>Seq1
actgcagtctga
>Seq2
actggact

With Biopieces and add_ident:

read_fasta -i input.fa | add_ident -k SEQ_NAME -p Seq | write_fasta -o output.fa -x