The lefty walked five and struck out 10, but only lasted 6 1/3 innings after tiring out and losing command during his final two frames. It's the 16th game of his career reaching double-digit strikeouts and the first time since July 23, 2012 against the Cubs when he was with the Pirates.
Since 1916, only one other team has scored four-plus runs while recording one or fewer hits, that coming in 1990 when the White Sox beat the Yankees, 4-0, despite getting no hits.
Only five previous pitchers in baseball history had thrown six-plus innings without a hit and allowed at least two runs, the last being Matt Young with the Red Sox in 1992.
"It's tough to take, but I battled for six innings and kept the team in the ballgame," said Bedard, who didn't seem fazed by losing with a no-no intact. "It was a grind later on."
The Astros were doubled up on the scoreboard despite outhitting the Mariners, 7-1. It was the second straight night Houston lost by multiple runs while posting at least five more hits than Seattle.
"I would say probably the strangest game I've been involved in from little leagues to the big leagues," said Houston manager Bo Porter. "Where you give up one hit and punch out 15 guys and end up on the losing side."
The Astros have now lost eight of their past nine at home and their last 12 games in Minute Maid Park against American League West foes.
With the Astros up 2-0 entering the sixth, Bedard walked Saunders and Brad Miller with one out before they advanced a base on a passed ball. Seattle second baseman Nick Franklin brought Saunders home with a sacrifice fly to center and Miller scored on another passed ball to tie the game.
Despite having over 100 pitches already, Bedard went back out for the seventh, but walked Justin Smoak after retiring Kyle Seager, ending the lefty's night.
According to Porter, Bedard was ready to leave the game.
"The plan was to see if he could have a quick inning," Porter said. "He was at the end of the rope. When I went out there with a chuckle and left it up to him, he just said, 'I'm done' and flipped the ball at me. At that point, I took the ball."
Bedard confirmed that there was no desire to continue at that point, with 109 pitches, even though a no-hitter was still a possibility.
"I've had three shoulder surgeries, so I'm not going over 110," he said. "I'd rather pitch a couple more years than face another batter."
The walk to Smoak ultimately ended up costing him the decision, as the Mariners first baseman was the first run of the inning, tagging him with the loss.
Jose Cisnero entered and walked a batter before serving up Saunders' go-ahead double that just eluded Brandon Barnes' glove on Tal's Hill in center field.
The Astros were mostly at the mercy of Seattle All-Star starter Hisashi Iwakuma, who pitched around some early threats to earn the win with seven innings of two-run ball.
He never had it easy, beginning in the third, when Houston put runners on second and third with no outs. Consecutive strikeouts and a hard-hit Jose Altuve liner that Iwakuma nabbed ended the threat. The Astros left two more runners on in the fourth.
"Again, you talk about the critical strikeouts," Porter said. "Tonight's game is a prime example of how you lose baseball games. There are critical strikeouts that are more vital when you are in position to put the ball in play and score runs. From a situational standpoint, we didn't get it done."
Bedard cruised through four frames, retiring the first 12 Mariners as his off-speed stuff left Seattle hitters baffled.
The Astros gave the southpaw his big break in the fifth. After being so frustrated the prior two innings, Altuve's sacrifice fly and Jason Castro's RBI infield single provided Houston a 2-0 edge.
But the command Bedard had used to fool hitters and cruise past a hot-hitting Mariners lineup evaporated, leading to the combination of errant pitches and walks that earned him a strange loss despite pitching an abbreviated no-hitter. He's now lost his last four outings and is 3-7 for the year.
"That was one of the odder wins I've ever seen," Saunders said. "[Bedard] was getting ahead in counts and keeping us off balance. Later in the game, we were able to work our walks and we've been doing that great as of late. Getting runners on ... we were able to manufacture a couple runs with no hits, which is pretty surprising."
Bedard is just the second Astros pitcher to finish 6 1/3 hitless innings without completing a full no-hitter. Don Wilson also did so in September 1974 against Cincinnati.
The Astros were looking for the 11th no-no in club history and their first since six Houston pitchers combined to blank the Yankees in 2003.
But instead, it was Seattle that emerged with its fourth win in the past five games against the Astros, giving it a 6-5 edge in the season series.