Phelps connected with one out in the 11th inning for a three-run shot that gave Cleveland a 5-2 victory and a three-game sweep over the Pittsburgh Pirates on Sunday.
"That's my first walk-off of any kind, at least that I can recall," said Phelps, who was mobbed at the plate by teammates. "That was awesome. Really cool."
Carlos Santana also homered for the AL Central leaders, who improved to 23-12 at home by pulling out a game that was delayed by rain in the eighth inning for 1 hour, 57 minutes.
"I guess it was worth the wait," manager Manny Acta said of the Indians' eighth win in their last at-bat at Progressive Field.
Shin-Soo Choo singled off Tim Wood (0-1) with one out in the 11th for his third hit and stole second. Wood intentionally walked Santana to face Phelps, who came up hitting .100 (2 for 20) since being called up from Triple-A Columbus on June 8.
"It was a fastball in," Wood said. "He did exactly what he's supposed to do with a belt-high fastball. My sinker's my best pitch. I had faced him a few times (in the minors) and got him out."
Tony Sipp (3-0) worked a scoreless 11th to help the Indians win for the fifth time in seven games and move to 6-0 in interleague play. Their sweep extended the Pirates' losing streak to 13 games in AL ballparks. Pittsburgh has not won a road interleague game since June 17, 2009, at Minnesota.
Sipp and five other relievers worked six scoreless innings. Cleveland's bullpen has not allowed a run in 22 2/3 innings over seven games.
The offense has been another story. Before the game, the Indians announced that hitting coach Jon Nunnally had been replaced by Bruce Fields, the organization's minor league hitting instructor. Acta said the decision was made before Cleveland's 5-1 win on Saturday night.
"It was very tough, one of my toughest days of work," Acta said. "Yesterday we won the game and didn't feel like celebrating. I understand that some (players) are a little upset, but we have to do what's best for our team."
Phelps' liner into the right-field seats made Cleveland 1 for 7 with runners in scoring position Sunday -- and 18 for 116 (.155) since June 2.
Pittsburgh manager Clint Hurdle lamented the Pirates' offensive struggles, too. They totaled three runs in the series following a four-game winning streak. Prior to that, they scored four runs in going 1-3
"We left 14 men on base," Hurdle said. "At the end of the day, that's a lot."
Acta was much more upbeat following Cleveland's seventh sweep of a series of at least three games this year.
"How about that bullpen?" he said. "They kept us in the game. Oh, and by the way, a pretty good series."
Acta and other Indians could not stop talking about a defensive gem by Asdrubal Cabrera. The shortstop made a barehand stop of a sharply hit one-hopper on the outfield grass and threw out Brandon Wood in the top of the 10th.
"Half the dugout was saying it was the best play ever," Acta said.
Added Phelps: "That was nasty. I became a fan right there and said, 'Ohhhh!'"
Santana drove Jeff Karstens' first pitch of the second into the right-field seats for his ninth homer. Phelps doubled on the next pitch, moved up on a passed ball and later scored when Lou Marson bounced into a double play, tying it at 2.
Masterson, 0-5 in 10 starts since opening 5-0, gave up two runs and seven hits over five innings. He ran up his pitch count early, though he walked only one and struck out five. He threw 69 of 110 pitches for strikes.
Karstens was lifted after the delay in the middle of the eighth. Hurdle said the right-hander would have continued if not for the rain.
Karstens gave up one earned run and five hits over seven innings. He has not allowed more than two earned runs in a game since May 3, a stretch of nine starts.
The Indians retrieved Phelps' home run ball and presented it to him. He said he'll keep it awhile before giving it to his parents. ... The Indians said the last Cleveland player to hit a game-ending shot for his first major league homer was Ben Francisco on June 29, 2007, against Tampa Bay, according to research by the Elias Sports Bureau. ... Indians OF Grady Sizemore went 0 for 5 with four strikeouts. ... Acta made a nifty backhand grab of a woeful ceremonial first pitch from Pro Football Hall of Famer Joe DeLamiellure that was 8 feet short and 5 feet wide. ... The series drew 100,437 fans, Cleveland's largest three-game series total since September 2008. ... Pirates first-base coach Luis Silverio stayed in the game after being hit in the inner thigh by a foul line drive off the bat of Jones in the fourth.