The Sunil Chhetri-led side registered two victories and a draw in three matches after they were placed at the 97th spot in August.
India defeated Mauritius and held St Kitts and Nevis to a draw to clinch the Tri-nation football series before defeating Macau in an away fixture in the 2019 AFC Asian Cup Qualification third round.
India have dropped below the 100th spot for the first time since May.
Meanwhile, Germany displaced Brazil to take the top spot. The reigning World Cup champions rose one spot from last month's rankings while Brazil are currently placed second.
Current European champions Portugal climbed three rungs to the third spot while Argentina dropped one spot to the fourth position. Belgium, Poland, Switzerland, France, Chile and Colombia round off the top 10.
Iran continued to be the top ranked nation in Asia, although it dropped one spot to 25th. Japan are the second highest in the continent at 40th followed by Australia (50th), South Korea (51st) and Saudi Arabia (53rd).