Boston shortstop Julio Lugo can’t reach this high throw from catcher Jason Varitek as Arizona’s Eric Byrnes slides safely into second base with a steal in the fifth inning yesterday.

AP / Paul Connors

PHOENIX, Ariz. — The managerial wheels were turning yesterday.

And when it was all over and the Red Sox had suffered a 5-1 loss to the Diamondbacks, Boston manager Terry Francona had a few decisions to rehash.

For instance, in the seventh, Dustin Pedroia led off with a single with the Sox losing, 2-1. Eric Hinske had been in the on-deck circle, but after the base hit, Francona sent up Alex Cora to bunt instead of having Hinske hit, a strategy he had hatched before Pedroia stepped into the batter’s box.

Cora dropped down a nice sacrifice bunt, pushing Pedroia to second, but that left Boston with Julio Lugo and Coco Crisp coming up — and David Ortiz and J.D. Drew, who did not start, still on the bench. Lugo wound up 3-for-27 on the trip. Crisp was 3-for-5.

Francona said he had confidence in both of them, and thought Crisp was swinging the bat well yesterday. Neither one came through. Lugo hit a first-pitch bouncer to third. Crisp hit the ball on the nose, but flied deep to center.

Then, in the ninth, Ortiz (11 homers, 42 RBI, .330 batting average) never got off the bench. Drew and Hinske each pinch hit in the inning. A walk to Hinske brought up Lugo. Still Ortiz sat. Lugo got an infield single, putting two on with two outs. Crisp was next. Francona let Crisp bat, and the result was a game-ending flyout to center with Kevin Youkilis on deck and Manny Ramirez in the hole.

“David could have hit one off the roof and it wouldn’t have mattered, we still would have been behind,” said Francona. “We still had David sitting there for later. He could have hit for [Jason] Varitek [batting behind Manny].”

A rare protest

Ramirez, who had missed Saturday night’s game because of a sore left wrist, the result of being hit by a pitch the previous night, was upset with plate umpire Chris Guccione in the fifth.

Ramirez waved at a 3-and-2 down-and-away slider from Randy Johnson and tipped the ball. Guccione called it a foul tip and strike three, ending the inning with a runner at first. Ramirez protested that the ball had hit the dirt before being gloved by catcher Chris Snyder. First-base umpire Chad Fairchild, when asked, backed up Guccione’s call.

Still, Ramirez wasn’t convinced and uncharacteristically demonstrably pleaded his case before being pushed away from Guccione by third-base coach DeMarlo Hale as Francona came out of the Boston dugout to pick up where Ramirez’s argument had left off.

Lowell nursing sore thumb

Third baseman Mike Lowell has a sprained left thumb, a nagging injury he suffered a week ago Sunday while trying to make a diving play at home against the Yankees.

He and the training staff figured out a way to tape it so he has protection and mobility. Lowell, who lofted the game-winning sacrifice fly as a pinch-hitter Saturday night, delivered Boston’s only run yesterday, with a ringing double inside the third-base bag in the fourth, winning a nine-pitch battle with Johnson.

Still, it probably isn’t just coincidence that he has a sprained thumb and went 2-for-20 on the trip, dropping his average from .333 to .312.

Umpire calls obstruction

Crisp was able to make a positive out of a negative in the first inning.

After lining a one-out single to left, Crisp, wanting to steal second base, was trapped off first base when Johnson’s first move was a throw over there instead of a pitch to the plate.

Crisp was caught in a rundown. When first baseman Conor Jackson threw the ball to second baseman Orlando Hudson, Jackson, trying to get out of the way in the rundown, made contact with Crisp, who was very wide in the infield dirt.

Fairchild called obstruction on the part of Jackson and awarded Crisp second base, leading to an argument from the Diamondbacks that went nowhere.

But then, neither did Crisp. He was unable to advance past second as Johnson pitched out of trouble.

Crisp was not charged with a “caught stealing” as per rule 10.07 (h).

Around the bases

The roof, which was open the first two nights of the series, was closed for yesterday’s game with the temperature outside at 94 degrees for the first pitch at 1:40 p.m., local time. … In each game, there were times when it seemed as if it were a home game for the Red Sox given the loud ovations for “Yooooook” [Youkilis], not to mention the “Let’s Go Red Sox” cheers that reverberated around the ballpark. The Diamondbacks fans tried to shout down the Boston fans, including a “Let’s Go D-Backs” cheer that followed the “Let’s Go Red Sox” cheer. … Pedroia was given the first intentional walk of his big-league career. First base was open with two outs in the fourth and Matsuzaka on deck, so Johnson, who had fanned Pedroia in the second, issued him the free pass.

skrasner@projo.com