Alou had said earlier that Bonds was also questionable for Wednesday night's series-closing game here. The Giants then have a day off Thursday before opening a three-game series against the Mets in New York on Friday night.
"I was looking to give him two days off," said Alou, who originally had penciled Bonds into Tuesday night's lineup with the proviso that the left fielder could take Wednesday night off. "And it could turn into three days off."
Bonds, who missed all except 14 games last season after having his right knee surgically repaired three times, has started 40 of the team's first 52 games, many more than was originally contemplated when he returned full time for his 21st season. He had just finished a stint of nine starts in the team's last 10 games and said he may be ready to go again.
"I'll probably take the two off, but I'm not sure right now," said Bonds, who felt revived enough that he was preparing to pinch-hit in the ninth inning Tuesday night. "Sometimes one is enough."
Bonds said Sunday before taking the field against Colorado that he was plagued with soreness in his back and knee. To that end, his personal trainer, Harvey Shields, worked on him as he laid prone on the floor in front of his locker right up until game time. The team chiropractor also has been working with Bonds, who spent much of that session writhing in pain as Shields tried to work out the kinks.
When asked at the time why he didn't sit out that game, Bonds said: "I've never been a quitter."
Bonds wound up playing in the last game of that homestand and had a single off the right-field wall, a walk and the milestone homer in four plate appearances. On Monday night, he singled in his first at-bat and went 1-for-4.
Bonds is now 40 homers behind Hank Aaron, the all-time leader with 755. He has hit only two of his seven homers on the season in his last 73 plate appearances -- No. 714 on May 20 at Oakland and Sunday's No. 715. He said Monday that he's contemplating coming back next season if he's healthy.
Alou said Tuesday's need to scratch Bonds will probably signal a new phase in how he will spot the 41-year-old in the starting lineup. No one expected Bonds to take the season's first 50 games to pass Ruth, Alou said.
"Hitting those homers -- 714 and 715 -- was part of the reason he played more games," he said. "I think now we're entering a period of time where everything needs to calm down. We're probably going to have to manage Barry differently. We'll have to pay more attention to the long flights, flying six hours. [Monday] night, I knew he was suffering on those last two at-bats. And I knew why -- flying into town in those early-morning hours."
The Giants flew overnight from San Francisco after Sunday's game and arrived in the wee hours of Monday morning. Still, Alou asked Bonds to play in that evening's game -- a 5-1 loss to Florida -- and after a closed-door meeting between Bonds and the manager, the left-handed hitter agreed.
"I could have sat out," Bonds said Monday. "It was up to me. But Felipe said we needed to try and win that game."
In late April, Alou and Bonds were faced with a similar prospect. Bonds' knee and left elbow were swollen. And after Bonds had played games in six successive days, Alou rested him on back-to-back nights in Arizona on April 19 and 20.
Bonds hit his first homer of the season April 22 in Colorado. He had missed only five games since then until sitting out his sixth Tuesday night as he struggled to tie and pass Ruth.
The Giants have looked lackluster the last two games and Alou promised to shuffle the lineup Wednesday.
"There's no life here, either in the dugout or in the stands," he said about two games that have been played in front of a combined crowd of 17,872.
Alou said he intended to give right fielder Randy Winn a breather, which means that if Bonds sits again, the Giants will have an outfield of Mark Sweeney, Steve Finley and Jason Ellison. Sweeney was moved from first base to left field Tuesday night after Bonds was scratched.
Lance Niekro, the regular first baseman who came off the disabled list Tuesday after a bout with bursitis in his right shoulder, subbed for Bonds and, with a pair of homers, had his first multihomer game as a Major Leaguer.
"He was fresh," " Alou said. "A bunch of guys don't want to admit it, but they are tired."