The South African had recently expressed his concern that a long-term deal was taking too long to sort out, and he feared the agreement Everton had with Borussia Dortmund would run out before the fee had been agreed.
Pienaar signed on loan in July last year, and Everton had to pay the £2.05million fee before the end of this season or they could have been forced to renegotiate a higher figure.
But Everton have confirmed that Pienaar has signed a three-year deal, keeping him at Goodison Park until July 2011.
Pienaar, 26, has impressed Everton fans with his ball skills and willingness to work hard on the flanks, and he was a key figure in the club's progress to the Carling Cup semi-finals and the last 16 of the UEFA Cup.
Moyes said: "Steven has done well for us. He is one of the reasons our football has improved. He is a really good football player."