Wayne made the catch with less than 10 minutes remaining in the game, stooping low to collect a 21-yard pass from quarterback Andrew Luck.
The 34-year-old became only the ninth player in history to reach the 1,000 catches landmark and moved into eighth on the all-time receptions list with his 1,001st catch later in the match.
"It's a great honour," Wayne told The AP. "It's a humbling experience to be in an elite class with a bunch of guys who have helped pave the way for guys like myself.
"I wish it was more of a greater celebration. I would rather take the W (win) than any accolades."
Wayne is still some way behind top spot in career receptions, a position currently held by Jerry Rice with 1,549 catches.