Bautista's hitless streak reached six games on Monday as the Blue Jays fell 3-1 to the Boston Red Sox at Rogers Centre.
"He's squaring some balls up, he was on a nice little roll but that's what hitting is," Gibbons said. "You go through peaks and valleys.
"Good pitching can shut down good hitting, not all the time but a lot of the time."
Bautista, currently mired in an 0-for-20 slump and batting .238 for the season, hasn't gone this long without a hit since June 2010.
As a whole, the Blue Jays have scored one or fewer runs in three of their past five outings despite averaging 5.5 runs per-game heading into Monday.
Right-hander Clay Buchholz (6-6) didn't make it easy on the Toronto lineup, allowing only five hits and one earned run with five strikeouts through eight innings of work.
He tossed 96 pitches — 68 for strikes — to outduel R.A Dickey for the victory.
"I like pitching here. I like the mound here," said Buchholz, who has 10 career wins against Toronto. "I feel good pitching here and have my whole career."
Added Gibbons: "Buchholz was on tonight. We've seen him like that before. He's tough."
Xander Bogaerts had a two-run double for the Red Sox (35-43) and Mookie Betts cashed in on a single from Brock Holt.
Dickey (3-8) went six innings for Toronto, allowing six hits with three walks, three strikeouts and three earned runs.
The knuckleballer opened the third inning with a walk to Jackie Bradley Jr. Betts followed with a single and Dickey issued another walk to Holt to load the bases with nobody out.
Bogaerts then took the first pitch he saw over the head of Bautista in right field for a two-run double and the game's first runs.
Dickey got the next three batters to pop up, stranding runners on second and third.
Despite the loss, Dickey pitched his fourth straight quality start.
"I'm kind of in a stretch where I'm pitching just good enough to lose," said Dickey. "I feel I'm capable of more. … The two pitches I got hurt on today were poorly executed fastballs."
Betts also got to Dickey, starting off the fifth with a triple. Holt sent him home on a bloop single to make it 3-0 Red Sox.
Toronto (41-37) finally got to Buchholz in the bottom of the sixth inning for its first run of the game.
After starting off the inning with a single, Devon Travis moved to second on a fielders choice and then came home on a double from Josh Donaldson.
Toronto nearly scored the game's first run when Kevin Pillar hit a double to left field in the bottom of the second. Russell Martin thought about going from first to home on the play but pulled up after passing third and was eventually tagged out by Pablo Sandoval to end the inning.
"He was trying to stop (at third)," said Gibbons. "Left field's Satan's corner when you're trying to score a guy from first base. … He lost his balance."
Liam Hendriks came on in relief for the Blue Jays to start the seventh and retired five in a row before Brett Cecil finished the game.
Boston's Koji Uehara worked a 1-2-3 ninth inning for his 17th save of the season.
The loss drops the Blue Jays to 6-4 this season against their division rival Red Sox, despite Boston sitting last in the A.L. East. Just one game separates four teams in the division for top spot, with Baltimore holding down first place over Tampa Bay because of percentage points.
Toronto plays Boston three more times in the series.
"It's in your division, you play them so many damn times so you have to beat them," said Gibbons. "Our division is some kind of bunched up right now."