After beating Arizona earlier this month with a pinch-hit grand slam, Howard lined into a double play as a pinch-hitter in the ninth off closer Jose Valverde to end a Philadelphia rally.
That allowed the Diamondbacks to hang on, giving this matchup of the aging lefties to the Big Unit.
Johnson returned from tendinitis to toss one-hit ball over six shutout innings, and Eric Byrnes homered twice to lead the Arizona Diamondbacks to a 4-3 win over Jamie Moyer and the Phillies on Wednesday night.
Arizona swept the three-game series and extended its winning streak to seven games.
"There's too much talent in here to not think they're capable of doing that," Johnson said.
The 43-year-old Johnson (3-2) missed his last start with tendinitis in his forearm, though it was tough to tell anything was ever bothering him. He allowed only Pat Burrell's second-inning single, walked none and mixed a sharp slider and his 90-plus fastball to strike out six.
The five-time Cy Young winner blamed a 10-day layoff on why his back stiffened late in his 61-pitch outing.
"I knew I was good enough to pitch," Johnson said. "The first couple of innings I was kind of reluctant, kind of hesitant of letting things go. As the game progressed, I started getting better."
Howard was held out of the starting lineup a night after suffering a cramp in his left leg. Howard said he was OK, but the slugging first baseman also has never faced Johnson.
Manager Charlie Manuel tried to rest Howard the last time the Phillies faced the 6-foot-10 lefty. That lasted until the seventh when Howard hit a pinch-hit grand slam against Arizona's bullpen to win the game for Philadelphia.
Howard had a chance to win it again because reliever Brandon Lyon faltered in the ninth.
Arizona brought in Valverde to stop the rally, but Burrell singled home Rollins with one out to make it 4-3 and Howard pinch hit for Wes Helms.
After pinch-runner Michael Bourn stole second, Howard hit a line drive to Hudson stationed in short right field against the lefty slugger and Bourn was easily doubled off to give Valverde his 19th save.
"I knew he was over there," Arizona manager Bob Melvin said of Howard. "It was just a matter of time until we were going to get him."
Howard said once he hit into the shift, he realized his liner, "wasn't going to fall."
The Phillies lost their third straight and fell back under .500 after going over the mark for the first time all season on Saturday.
"I'm concerned about our team. I'm worried," Manuel said. "We've got to improve and stop making mistakes."
Former Seattle teammates Johnson and the 44-year-old Moyer (5-4) combined to set a record for the matchup of the oldest lefties in history. At a combined 88 years, 90 days, Johnson and Moyer broke the record set the last time these two faced off in early May.
Moyer earned the win in that game, but was done in by home runs in this one.
Byrnes hit his seventh homer of the season on the first pitch of the game, then went deep in the eighth on the first pitch of the at-bat.
Moyer -- who allowed eight hits in 7 2/3 innings -- was chased after rookie Mark Reynolds hit a two-run shot for a 4-0 lead. Reynolds has four homers in 54 at-bats since being promoted from Double-A on May 16.
Once Johnson more comfortable, he went on a strikeout binge, starting with Aaron Rowand to end the third inning.
"I was looking forward to getting my work in and getting back into my routine," Johnson said.
Victorino advanced to second on shortstop Alberto Callaspo's throwing error to open the fourth inning. No problem for Johnson.
He struck out Rollins and whiffed Chase Utley. Then Johnson doubled his age on an 86 mph slider that Burrell swung and missed at for strike three.
When Johnson struck out Helms leading off the fifth that made it five Ks over six batters -- all swinging.
"That was a new Randy Johnson tonight," Rollins said. "He had a real good slider, not a real good fastball, but he was hitting his spots."
- Reynolds was back in the starting lineup, a night after suffering what manager Bob Melvin called a "serious stinger" from a collision with pitcher randon Medders.
- SS Stephen Drew was not in the lineup after he got nailed in the left shin on a hard slide by Utley on Tuesday. Melvin said Drew was banged up, but was available to pinch hit.