Michael Jacobs’ deflected shot won it at the death for the Blues at a freezing Priestfield, to close the gap on the play-offs to two points.
That sparked jubilant scenes on the final whistle as players, staff and 1,475 travelling fans celebrated.
Cowley felt digging out the success against a physical side without a recognised centre-half made the win the finest this term.
He said: ‘It was a super win, really good win.
‘I think we’ll have more free-flowing performances than that one, but it’s very difficult to come here on a three-game week after expending so much energy already.
‘To come to a physical, direct side like Gillingham, who I haven’t seen a side play fluently against this season, was pleasing.
‘They compete really hard and turn it into a fight.
‘You have to be good enough to compete.
‘We maybe didn’t have the rhythm but it was a magnificent effort.
‘So to find the winner in stoppage time was a brilliant feeling.
‘For me to come to a really direct side with no centre-halves makes it the best win of the season.’