Marco Canola (Bardiani-CSF) John Murphy (UnitedHealtcare), Thomas Sprengers (Topsport Vlaanderen-Baloise) and Preben Van Hecke (Topsport Vlaanderen-Baloise) had opened up a 3:30 gap over the peloton after 100 km.
However, Sky and Omega Pharma-QuickStep worked in tandem to reel them in.
Froome made his move with 1.5km to go and takes the GC lead into the final day's racing with a second consecutive win at the Tour of Oman in his sights.
Tejay van Garderen (BMC) took second with Rigoberto Uran (Omega Pharma-QuickStep) in third.
“It feels absolutely fantastic getting that win today, especially with it being my first race of the season.
“Coming into the race I wasn’t sure exactly where my form was but this has proved I’m where I need to be right now," Froome said
Stage five result
1 Chris Froome (GBr) Sky
2 Tejay van Garderen (USA) BMC
3 Rigoberto Urán (Col) Omega Pharma-QuickStep
4 Joaquim Rodríguez (Rus) Katusha
5 Robert Gesink (Ned) Belkin