Pietersen will lead England in the fourth Test against South Africa at The Oval, which starts on Thursday.
"Kevin's got his way of playing and we encourage him to play that way," Moores told BBC Radio 5 Live.
"We'll have different views, as a coach and captain should, but we want to play aggressive and positive cricket."
Pietersen was unveiled as England's Test and one-day skipper following the resignations of Michael Vaughan and Paul Collingwood on Sunday.
And Moores, speaking for the first time since Pietersen's appointment, said the South African-born batsman had been the overwhelming choice for the job.
"It's always a close decision when it's something as big as the England captaincy," said Moores, who spoke to Pietersen at length before the 28-year-old was offered the job.
"But we felt he could do a really good job. Don't under-estimate Kevin, he didn't get to where he is as a player without being a deep thinker on the game and being able to think clearly.
"The 94 dismissal [in the third Test at Edgbaston, when Pietersen was caught attempting to hit a six] has been talked about a lot, but we had to take the game to them at that stage.
"We were under pressure and his partnership with Paul Collingwood was crucial in getting us to that target of 280 which gave us a great chance of winning the game."
Moores also denied that a rift had opened between himself and Pietersen's predecessor in the weeks before Vaughan's resignation.
It has been widely reported that Vaughan was unhappy with the selection of Australian-born seamer Darren Pattinson for the second Test at Headingley.
Moores said: "We were building a relationship. The press will speculate because we've changed captains.
"We'd had a run as selectors of being very consistent, although we made some tough decisions, like bringing in Stuart Broad and James Anderson in New Zealand.
"As selectors you're not always going to be right, and Darren Pattinson actually performed OK for a guy on debut under pressure."
Moores added that he expected Vaughan to fight for his place in the England team after taking a short break from the game.
"He's still a fine cricketer, it's key now he has a break, has a chance to recharge the batteries and fight to get back in the team as England a batsman," said Moores.
"The hunger is still there to do great things for England, it's not that long ago he was scoring a fantastic hundred against New Zealand.
"He had spoken in the months before about the challenges of captaining England and getting his batting right and the cumulative pressure of that.
"After the game [at Edgbaston] we sat down to discuss preparation for the next Test match and he said it was time to step down and give somebody else a go.
"I respect that and I respect the work he's done over the last five years."
Vaughan has been replaced in the 13-man squad for the final Test by Essex all-rounder Ravi Bopara, although Moores admitted Middlesex's Owais Shah had been unlucky to miss out.
"It was a tough one, we've got a few good players out there," said Moores.
South Africa coach Mickey Arthur has warned his side to be prepared to face an England side he described as being "like a wounded lion" under Pietersen.
"We are expecting a huge backlash from England," he said. "They have new leadership, a new direction, they are all going to want to impress KP, so we are expecting a really tough challenge.
"KP is going to bring a lot to the job; he has had challenges thrown at him all along the way and he has always seemed to come out doing really well - he seems to thrive on it.
"It will be a huge challenge to him. Does it affect his batting? What is his vision going to be?"
Meanwhile, Shane Warne says his former Hampshire team-mate Pietersen will need to "reconsider his whole outlook" as he begins his term as skipper.
The great Australian spinner told the Times: "Kevin Pietersen now stands at a crossroads in his life as well as his career.
"Being England captain will take up more time than he can imagine and he will need to reconsider his whole outlook.
"Within the game worldwide he has a reputation as being an individual, but to be successful a leader must be a giver not a taker - to his team, fringe players, sponsors, the public, everyone."
"Hopefully his captaincy will be similar to his batting: positive, instinctive and entertaining."
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