Most likely, he destroyed the two ships before Fujitora could get to him. Since the Marines weren't able to confirm his death, it's likely he fell into the ocean when battling Fujitora and was saved by one of his subordinates. It may have also been that Fujitora was the only one he actually faced as well, since there were no real report of all of the Marine envoy taking him on together and it may be that Sengoku's sudden physical ageing from the timeskip has lead to such a decrease in strength for him to not be of use in his base form while his Daibutsu form wouldn't really be usable on a ship. The most recent chapter shows Jack as a fairly mediocre fighter for a Yonko Commander with him getting easily caught off-guard by Shutenmaru, so I doubt he had much strength, ability or strategy that got the better of the Admiral.
