It was a heartbreaking way to end what would have been a memorable comeback for the Saints, who had found themselves 11 points down after just 15 minutes, and although Mallinder praised the way his team fought back into the contest he also acknowledged that they allowed Saracens the opportunity to win the game thanks to two Owen Farrell penalties.
"It is tough to take," he said in his post-match comments. "I thought the effort was great from the boys. We kept our nerve and fought our way back into it. But we let them back into the game instead of closing things out.
"The last 10 minutes were crucial. There were two or three key decisions from the referee, and at this level they were the difference between winning and losing.
"There's not a lot between the top teams in the Aviva Premiership and we're still very much in it despite being mid table. There is a long way to go and we're looking forward to the second half of the season."
This was the fourth match in an extremely tough run for the Saints which has also included home and away games with Ulster in the Heineken Cup and Aviva Premiership Rugby clashes with the league's two top teams. Up next for the Saints are Exeter - who are always difficult to play at Sandy Park - before the crucial Heineken Cup Rounds 5 and 6 matches against Castres and Glasgow.
However the Saints boss is still optimistic about the next few weeks and months.
"2012 has been a year of highs and lows," Mallinder commented. "We've beaten Gloucester [the only loss inflicted on the Cherry and Whites at Kingsholm], Bath [lost only twice at home] and Ulster away [the Irish province's first home European loss in four years] and shown that we're a good side. But we need to be consistent and build going into the rest of the season."
Nearly 19,000 fans turned stadiumMK into a cauldron of noise, with three sides of the stadium a sea of black, green and gold, and Mallinder also thanked the fans for their support, adding: "We've got terrific fans who follow us. Today I thought they were fantastic, really getting behind the team throughout the match and making themselves heard."