An engine valve control system for controlling engine valve lift during an automatic transmission shift. A plurality of engine valve actuation systems are each coupled to an individual engine valve for electronically controlling valve lift. Each valve actuation system includes a hydraulically operated piston coupled to each of the engine valves, and an electronically actuated supply valve responsive to a supply signal and coupled between the hydraulically operated piston and a source of hydraulic fluid, and an electronically actuated drain valve responsive to a drain signal and coupled between the piston and source of hydraulic fluid. A controller responsive to a shift command from a transmission controller, provides the supply and drain signals in appropriate timing and phase relationship to reduce valve lift during the automatic transmission shift. In another aspect of the invention, the controller also reduces the hydraulic coupling force applied to the clutch elements during an automatic transmission shift.