Lowrie, who had been sidelined since June 17 with a left shoulder strain, batted eighth and played third base. Scutaro batted ninth and stayed at shortstop.
Third baseman Kevin Youkilis got the night off. Amid a busy portion of the schedule when the Red Sox won't have had any days off between July 22 and Aug. 11, Francona is trying to rest regulars when he can.
Dustin Pedroia might get a rare night off on Wednesday, which, coupled with Thursday's team day off, could give the second baseman a nice respite.
Pedroia batted cleanup Monday, a spot in the lineup he has thrived in whenever Youkilis has been out. Carl Crawford, who has been red-hot of late, batted second.
The return of Lowrie gives the Red Sox a switch-hitting bat with power, not to mention a player who feasts against lefties.
"It's great for us," Francona said. "Shoot, the first six weeks of the year he was our best hitter, our most productive hitter. We don't have to have him play every day. He plays third tonight -- he'll probably play short tomorrow. We'll see how he does tonight. It's nice to have him and Scoot together. I think it will give us a lot more production."