The Saddlers had a successful first half, taking the lead through Elijah Adebayo, but were pegged back by a Liam Feeney strike.
In the second half Walsall impressed with a dominant showing, netting again through Wes McDonald and Dan Scarr, and Clarke was delighted to see the goals flowing.
When asked about the performance, Clarke said: “It was on par, potentially, with the Newport performance with a clinicalness about us.
“That’s what we’ve been asking for and to cut out the individual errors.
“I’m really pleased that we got three goals on the front foot. We created many opportunities against a team in form.
“We’ll take that, three points.”
Walsall have had other impressive performances this season but failed to put chances away.
On Merseyside the Sadders had 13 shots on target and could have built on their three goals, something that Clarke is still frustrated with.
“We worked well from the front and the game plan worked nicely today,” Clarke.
“We had those areas where we were a little bit more clinical.
“Albeit I’m still frustrated we didn’t get a few more, to be honest. There were opportunities to make the game a little bit more comfortable. Tranmere are a good team and they kept going.”