Donnie Murphy connects for a go-ahead, two-run homer in the top of the 13th inning for Florida. (JONATHAN ERNST/REUTERS)

There will come a time when Stephen Strasburg will death-stare, or worse, any manager who would dare yank him from a tie game after six innings and only 61 pitches on a cool September night when the season is dwindling down to a few precious weeks. But that time was not Saturday night, and this version of Strasburg, still feeling his way in a post-surgical world, could only grudgingly accept the congratulatory, end-of-a-day’s-work handshakes in the Washington Nationals’ dugout at what would turn out to be not even the midpoint of the game.

Someday, Strasburg will be permitted to stay out there to pitch the seventh, the eighth and even the ninth. But he will never be left out there to pitch the 13th, which is when this game ultimately was lost. A crowd of 33,247, drawn largely by the prospect of Strasburg’s third start of 2011, saw a valiant effort by the Nationals’ bullpen fall short, as the Florida Marlins finally broke through in the top of the 13th to swipe a 4-1 win.

“I’m going to go out until they tell me I’m done, bottom line,” said a subdued Strasburg.

Collin Balester, the Nationals’ sixth pitcher of the night, in his third inning of work, gave up the decisive runs in the 13th — a two-run homer to Marlins shortstop Donnie Murphy, then, three batters later, an RBI double by Mike Stanton. That broke a string of 24 straight scoreless innings by the Nationals’ bullpen, a quarter of which were amassed Saturday night.

The Nationals entered the day tied for third with the New York Mets in the NL East, but the loss left them only three games ahead of the last-place Marlins. Stunningly, the Nationals are 4-10 against the Marlins this season, including five straight losses, and are 8-26 against them at Nationals Park since its opening in 2008. At 71-79, they must go 10-1 over the season’s final 11 games (there was also a rainout that will not be made up) to finish above .500.

Ballester had already delivered two hitless, scoreless innings — following scoreless frames by Henry Rodriguez, Todd Coffey, Drew Storen and Sean Burnett — when Manager Davey Johnson sent him back out for a third. There was no one warming up, despite the presence of six other relievers on the expanded September roster. Tyler Clippard was unavailable after a heavy week of use. Some relievers were being held in reserve for Sunday. The 13th was Balester’s.

But Marlins catcher John Buck singled to left, and two batters later Murphy, a 28-year-old journeyman who had spent most of this season in the minors, yanked a 1-1 pitch over the wall in left. Stanton’s missile that plated the third run of the inning was similarly smoked, nearly knocking over the wall in left-center.

“I felt good. I’ve [pitched three innings] before,” Balester said. “I just a pitch up to Murphy, and he made me pay for it.”

The mini-gem by Strasburg that was sullied by what followed went like this: Six innings, four hits, one earned run, no walks, three strikeouts.

Strasburg hit all the benchmarks you would hope to see from him — one start after causing some alarm with a one-inning stretch of 92s and 93s on the radar gun, his fastball remained in the 95- to-97-mph range throughout the game, topping out at 99 mph. And aside from a couple of hanging curveballs, his command remains impeccable. In 14 innings thus far, he has struck out 11 batters without a single walk, and his ERA is a microscopic 0.64. And six innings, modest as it seems, still represents the most Strasburg has completed, in either the majors or minors, this season.

“He was great,” Johnson said. “He had a little chip on his shoulder when he went out there. He could’ve gone another inning, but I figured six innings was plenty.”

If you must nitpick, you can say that Strasburg doesn’t have the sheer, outrageous-K-rate dominance of his 2010 version, or that he never would have given up a double over the center fielder’s head to the opposing pitcher a year ago, as he did to Florida’s Chris Volstad in the second inning, leading to the Marlins’ only run against him. (That last part is true — he gave up only one hit in all of 2010 to the opposing pitcher, a single to the Chicago White Sox’s Gavin Floyd.)

Strasburg might have departed on the hook for a loss, except that Nationals catcher Wilson Ramos hit a leadoff homer off Volstad in the fifth, a rocket to left-center on a first-pitch fastball, to tie the game. It was Ramos’s 13th of the season, and his 12th as a catcher, increasing his franchise (2005-to-present) record. But they would not score again, stymied by Volstad and four relievers.

Strasburg’s three confrontations with Stanton, the Marlins’ 21-year-old power-hitting prodigy and a Nationals nemesis since his arrival in the big leagues on the same day as Strasburg (June 8, 2010), were epic, power-vs.-power battles, with Strasburg emerging victorious with a pair of strikeouts — one on an elevated, 99-mph heater that was Strasburg’s fastest pitch of the night — and a groundout.

Someday, when Stanton’s turn comes around again in the ninth, as it did Saturday night, it will be Strasburg on the mound to face him for a fourth time. But that time is not now.