Armstrong, after Monday's third stage, was still two seconds behind fellow American David Zabriskie for the overall lead. The top 10 remained unchanged following Monday's 133-mile trek from La Châtaigneraie to Tours.
Boonen outsprinted Austrian Peter Wrolich and completed the stage in four hours, 36.09 seconds. Australia's Stuart O'Grady was placed third after countryman Robbie McEwen was dropped to last for failing to maintain a straight line during the sprint to the finish.
Armstrong, seeking a seventh consecutive title, officially finished 88th in a time identical to the winner's.
Tuesday's fourth stage is a 41.9-mile team time trial from Tours to Blois.