Kristoff picked up his first victory of 2014 by winning a sprint finish after a 139km trek from Al Bustan to Quriyat ahead of Howard and Tom Boonen (Quick-Step Cycling Team) who was third.
With the peloton racing into a strong head wind, Kirstoff attacked early to avoid problems in the lead out and it paid dividends as he won by nearly a bike length.
Howard's second successive second placed finish meant that he picked up more bonus seconds and he holds a two second advantage in GC ahead of Kirstoff, stage one winner Andre Griepel (Lotto Belisol ) and Preben Van Hecke ( Topsport Vlaanderen – Baloise)
Defending champion and Tour de France winner Chris Froome finished safely in the peloton and is 12 seconds down in GC.
The riders observed a moment's silence before the start of the stage in memory of Belgian rider Kristof Goddaert, who died on Tuesday in a training accident.
Stage two result
1 Alexander Kristoff (NOR) Katusha, 3:12:01
2 Leigh Howard (AUS) Orica-GreenEdge, same time
3 Tom Boonen (BEL) Omega Pharma - Quick-Step, same time
4 Robert Forster (GER) UnitedHealthcare, same time
5 Nacer Bouhanni (FRA) FDJ, same time
1 Leigh Howard (AUS) Orica-GreenEdge, 7:15:20
2 Alexander Kristoff (NOR) Katusha, +2secs
3 Andre Greipel (GER) Lotto Belisol, same time
4 Preben van Hecke (BEL) Topsport Vlaanderen-Baloise, same time
5 Tom Boonen (BEL) Omega Pharma - Quick-Step, +8
6 Nicola Ruffoni (ITA) Bardiani-CSF, same time
7 Paolo Colonna (ITA) Bardiani-CSF, same time