The Liverpool pair played 90 and 63 minutes respectively at Wembley, where Harry Kane’s stoppage-time strike was enough for the Three Lions to guarantee first place in Group F.
Henderson had gone close to breaking the deadlock midway through the first half with a swerving low shot that was punched away by Slovenia goalkeeper Jan Oblak.
Kane eventually did net for the hosts, who can now officially begin planning their World Cup campaign next summer. Daniel Sturridge was an unused substitute.
In the same section, meanwhile, Andy Robertson and Scotland took a huge step in their pursuit of qualification for next year’s tournament in Russia by beating Slovakia 1-0.
The Reds left-back played the whole game at Hampden Park as Gordon Strachan’s charges beat the 10-man opposition courtesy of an 89th-minute Chris Martin winner.
Scotland therefore climbed to second position in the group and can make certain of a play-off spot if they claim victory in Slovenia on Sunday.
And in Belfast, Liverpool midfielder Emre Can was a second-half substitute in Germany’s 3-1 success over Northern Ireland - which assured the reigning champions of their return to the World Cup.
Philippe Coutinho clocked up 66 minutes for Brazil in their goalless stalemate with Bolivia, while club-mate Roberto Firmino remained on the bench.