After initially struggling to set consistent lap times, Checa finally found a reliable race pace and was fourth fastest in the final free practice session just before Superpole.
The Spaniard, who will start Sunday's races second in the points, went on to lap 0.835secs from pole sitter and world championship leader
Troy Bayliss.
"I'm quite satisfied with the Superpole result I set this afternoon," admitted Checa, who has never ridden at Monza before. "Coming where we started from this morning, we have improved a lot.
"We have been struggling with the setting of the bike in the qualifying sessions and have only been able to resolve it and find the right racing pace in the final part of the session.
"I find the track quite difficult to ride, but we are stepping up. There are still some areas in which we have to improve, like in the exit of the first chicane.
"Considering the start of the weekend I find the result positive and am confident we can have a good race tomorrow," he added.
Team-mate
Ryuichi Kiyonari started the day as one of the fastest men in the final qualifying practice, but nearly lost control of his bike twice during his Superpole lap and will start from the back of the second row on Sunday.
"The qualifying session this morning was a lot better for me then yesterday. The feeling with the machine is good and I start to understand the circuit a lot better and I have been able to improve my lap times," said the reigning BSB champion, also a Monza rookie.
"I'm a bit disappointed with my Superpole qualifying, but with a good start from the second row and fast first lap I can catch the top group and fight for a good result.
"The machine is perfect, the engine is fast, the set up is good, now I can only work on myself and try to ride more smoothly in the corners. In Valencia I had a good qualifying session but couldn't make it to the podium, tomorrow I will try and push hard for a good result and make that last step," he his declared.