After watching brilliant first-half goals from Chris Whelpdale and Deon Burton win a game of few chances, Allen was full of praise for the home side.
"I thought Bristol Rovers played really well," he said. "They were cheered off by their fans at half-time, despite being two goals down, and that says everything about their performance.
"I rang the Rovers chairman when I was out of work last year and pleaded with him to let me become manager because I like the club and the fans. There is something special about the atmosphere here.
"Whelpdale has that sort of goal in his locker and it was a magnificent strike. Burton also produced a moment of great quality. He has played at a higher level, but I gave him a chance when no one wanted him and he has repaid me by leading the line really well."
Rovers are improving under new boss John Ward and showed a lot of commitment. But the Gills matched it and defended their lead with tenacity after the break, restricting their hosts to few sights of goal.
Ward said: "I have no complaints. Gillingham had the edge on experience and it showed.
"But I can sleep well because my team gave everything.We are a young group and I have told the lads not to worry because if they continue to perform like that we will be okay.
"I am still looking to add new players and a striker is the priority. But we have a wage budget to consider. It isn't easy, but I have promised the supporters I will give everything to the job and that will also apply to the players over the months ahead."