The Three Lions secured a 3-0 series win at The Oval on Sunday evening, although the Three Lions fell 21 runs short of victory as the umpires called time due to bad light.
However, Flower believes that Cook is largely responsible for their victory thanks to his leadership skills.
"I think Cook's strong leadership was a key," Flower told Sky Sports News. "The players need to trust and respect their leader.
"He is a man they all look up to and he has a certain conviction and inner strength that will serve English cricket well."
"The strength that individuals have shown in pressure moments has been important. We must be better players by the time we take them on in November."
Cook was appointed captain in 2012.