The crucial moment of the game came as Warren Harris' low cross was met by Flood, who controlled the ball and saw his strike take a big deflection off a defender and find the bottom corner of Oliver Davies' goal. The goal helped the Rebels towards a fourth straight league win, ending Merthyr's 11-match unbeaten run in the process.
Merthyr will point towards a big penalty appeal in the first half, which was waved away by referee Ryan Atkin despite Kayne McLaggon appearing to be bundled to the ground by Smart.
"They should have had a penalty, it looked like a penalty from where we were", said Slough joint manager Neil Baker.
"It was a great three points. We were up against a very good side, and the two teams cancelled each other out".
Manny Williams came back into the side as the Rebels reverted to the midfield four that was so successful in recent wins against Leamington, Dunstable and Weymouth, though he was forced off with a groin injury shortly before the interval.
There was little to choose between the two sides in the first half. Manny Williams fired over in the second minute, and Chris Flood and Ian Traylor both headed efforts over the bar.
After Merthyr were denied a spot kick on 17 minutes, Williams again went close ten minutes later after Nathan Webb won possession, but his shot was off target.
Lee Togwell’s cross was almost turned into his own net by captain Ashley Evans minutes later, but Davies got down to make the save.
A double tactical substitution eight minutes before half time, with recent signing Jack Compton one of the replacements, improved the visitors and McLaggon really should have opened the scoring but he put a free header wide.
Merthyr started the second half well and continued to ask questions of the Rebels defence. Compton flashed a shot wide from 25 yards and left-back Scott Barrow saw two efforts from outside the box fly harmlessly over Scott’s goal before Flood broke the deadlock.
But Slough, with Smart and centre back partner Mark Nisbet in fine form, held firm and in truth Slough keeper Mark Scott had little to do. Merthyr' first shot on target came on 68 minutes, a 20-yard free kick from Compton which was held well.
The home side were denied in their attempts to extend their lead, with Davies keeping out Gavin James' shot after a fine through pass from Simon Dunn, and Nisbet putting a free header over from the resulting corner. Traylor created Merthyr's best opening with a great piece of individual skill which took him past two defenders, but Scott saved his fierce strike at the near post and Slough closed the game out.
Baker added: "I felt we were comfortable at 0-0, Merthyr weren't getting in behind us. With Gavin (James) and Chris (Flood) we always felt we would get chances, and one of them found the back of the net".
Merthyr Town Line up
Oliver Davies, Adam Davies (Corey Jenkins), Scott Barrow, Ashley Evans (c), Curtis McDonald, Scott Tancock, Ryan Prosser (Jarrad Wright), Kyle Copp (Jack Compton), Kayne McLaggon, Keyon Reffell, Ian Traylor. Substitutes not used: Kyle Patten, Eliot Richards.