Opening batsman Strauss saw his side lose their status as the world's number one Test side yesterday afternoon thanks to a 2-0 series defeat to South Africa.
Discussing that loss to the Proteas, Flower said that the ongoing saga regarding Kevin Pietersen's international was a contributing factor to the under-par performance.
As a result, Flower has tipped Strauss to recover from the disappointment.
"I think the last couple of weeks have been particularly draining on him. [The Pietersen issue] has certainly not helped and it's been a very unwelcome distraction during a very high profile and brilliant Test series," Flower told BBC Sport.
"He's tired after a hard-fought series. But he will re-energise. We know he's an excellent leader and can certainly take the Test team forward."
Strauss was appointed England captain in January 2009.