The pair are vying for favouritism ahead of the US PGA Championship at Oak Hill.
McIlroy felt the break was necessary for his “mental and emotional wellbeing” after a taxing 12 months.
Strong finish moves Tyrell Hatton into contention for AT&T Byron Nelson’s final round.
The Irishman finished two strokes clear at Woburn.
Stenson was stripped of the Ryder Cup captaincy after joining the Saudi-funded circuit last July.
Thomas is bidding to win his third US PGA title at a venue which last staged the event in 2013.
Spieth, who needs to win the US PGA to complete the grand slam, is suffering from an untimely wrist injury.
The South Korean Seung-yul Noh leads despite cracking his driver on the 12th hole.
Players have been fined up to £100,000 for each breach of the Tour’s regulations.
The American has struggled with his putter lately.