The 32-year-old was handed a four-month deal ahead of the India Test series after being dropped earlier this summer.
Pietersen was axed for England’s third Test match against South Africa after the batsman admitted to sending “provocative” text messages to Proteas players about his team-mates.
However, he impressed upon his return to the Test side as England secured an historic subcontinent series win, scoring a total of 338 runs.
“The contract won’t be a problem,” said Flower. “Kevin has been excellent in every way.”
“We did move on from it [the summer drama] as soon as we had our meetings and everyone made a commitment to do so.
“We don’t all always get on with people all of the time – any of us in any walk of life – and everyone has made an effort to make it work.
“It’s been really good fun and he should be very proud of the way he’s operated out here, both as an individual and as a player.”
Flower heaped praise on Pietersen for a particularly impressive knock of 186 in the second Test which helped inspire England’s comeback after their loss in Ahmedabad.
“For him to score as quickly as he did there and put such pressure on the opposition bowlers really helped us turn the series around,” added Flower.
“He’s been excellent in the field and in the dressing room.”
MORE: The latest football news
MORE: The latest tennis news
BIOGRAPHY: Cesc Fabregas