Quiet for much of the opening 45 minutes, the homegrown hero exploded into life with a well-taken winner in first-half stoppage time.
Dominic Calvert-Lewin assisted Rooney's opener and twice went close after the restart but the solitary goal proved enough for Everton to kick-off their campaign with a win for the first time in five attempts.
Everton had earlier struggled for fluidity as Ronald Koeman fielded five new signings from the outset, with Jordan Pickford comfortable in claiming a clean sheet.
Stoke looked bright in patches but, with only five teams scoring fewer goals last season, their troubles in attack still appear to need solving.
Both teams began with three at the back and it was the away side who looked more incisive early, targeting the space in behind Everton's wing-backs.
Mame Biram Diouf forced Pickford to push a wayward cross around his near post while the hosts were restricted to shooting from range throughout the opening 25 minutes, midfielder Idrissa Gueye twice trying his luck to little effect.
Stoke, without an opening day win since 2009, looked the likelier of the two to score before the end of a cagey first-half until Rooney rose high and headed Calvert-Lewin's delivery back across Jack Butland to the delight of the home fans.
Everton turned up the pressure after the restart and only a brave Kurt Zouma block prevented Calvert-Lewin from doubling the lead prior to the hour.
Veteran midfielder Darren Fletcher soon fizzed a reminder of Stoke's threat past the post although moments of promise were far too fleeting for the visitors.
Shifted higher up the pitch at half-time, Calvert-Lewin looked far more dangerous and drew a sharp low save from Butland.
Mark Hughes introduced last season's top scorer Peter Crouch and new signing Eric Maxim Choupo-Moting with around 20 minutes remaining but they struggled to create a clear opening in a repeat of last season's 1-0 defeat at Goodison Park.
Xherdan Shaqiri did find time to unleash one last-gasp shot that seemed destined to snatch Stoke a point but Pickford proved to be Everton's saviour, flying to his left to tip the goal-bound attempt wide and seal the points.
Key Opta stats:
- Wayne Rooney set a new Premier League record for the longest gap between two appearances for the same team (4837 days between Everton apps).
- Rooney also set a new Premier League record for the longest gap between goals for the same club (4869 days days between Everton goals).
- No player has scored more Premier League goals on the opening day than Wayne Rooney (8 - level with Alan Shearer & Frank Lampard).
- Rooney's goal was his 300th goal involvement in the Premier League (199 goals, 101 assists), only Alan Shearer (324) has more.
- Mark Hughes hasn't won any of his last seven opening day Premier League games (D2 L5) in charge of three different clubs in that time (Fulham, QPR and Stoke).