Waller threw a punch in the final flings of the game at Scotstoun, giving away a penalty at a time when Northampton had possession and were in search of the fourth try they desperately needed.
The 22-year-old’s heat of the moment reaction allowed Glasgow to regain possession and the home side made the most of it, scoring through Peter Horne to seal a 27-20 win in the final seconds.
For Saints it meant a Heineken Cup exit and the denial of a chance to even drop into the quarter-finals of the Amlin Challenge Cup.
But skipper Hartley, who was last month hit with a two-week ban for punching Ulster’s Rory Best, refused to criticise team-mate Waller.
“I think he knows,” said Hartley. “We’ve all been in that situation. I’ve been in that situation. I’ve given away silly penalties in my time and I think he’ll be feeling bad.
“But, like I said, it shouldn’t come down to that last minute, chasing the game. That game should have been sewn up before then.”
Unlike Saints, Glasgow, who had lost all five of the Heineken Cup Pool 4 games, showed a real cutting edge, taking chances when they came to them to clinch a fine victory.
Hartley was quick to give credit to the Rabo Direct PRO12 team and he praised their desire to win the game, rather than settle for a draw.
“I just think Glasgow were dangerous,” he said. “They weren’t really playing for anything other than home pride and they got a couple of opportunist tries and full credit to them.
“In the 80th minute they kept playing. They could have just kicked it out and we could have had a dead rubber but they played, they wanted to play and it made them dangerous.”